From owner-chemistry@ccl.net Fri Feb 4 01:18:00 2011 From: "ABHISHEK SHAHI shahi.abhishek1984,gmail.com" To: CCL Subject: CCL:G: Cannot generate a .cub file with G03 Message-Id: <-43860-110204005821-12299-Umg5wU1zJc42GSdLUaLaFw|a|server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=000e0ce07b90651df5049b6e91cf Date: Fri, 4 Feb 2011 11:28:14 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984(_)gmail.com] --000e0ce07b90651df5049b6e91cf Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: quoted-printable Hi, I would like to mention one more thing along with Jane that don't change th= e operating system or machine for .chk file. I mean don't carry your .chk file. After changing .chk to .fchk you can carry .fchk file anywhere. With regards; *ABHISHEK SHAHI* ** 2011/2/4 =D2=F3=BD=A1 janeyin600=3D-=3Dgmail.com > Yes, it works very well! I replaced "density=3Dscf" with "spin=3DQCI", th= en > I obtained the spin distribution right away. Thank you very much, Cheri! > > 2011/2/1 Cheri McFerrin cmcfer1^-^tigers.lsu.edu < > owner-chemistry/a\ccl.net > > >> hi jane: >> >> here is what i would do. run a single point energy using >> qcisd(full)/6-31g*. >> >> afterwards, run this command in order to convert your .chk file to a .fc= hk >> file >> >> formchk file.chk file.fchk >> >> next, run this command to generate a .cube file >> >> cubegen 0 density=3Dscf file.fchk 0 h >> >> more, on formchk and cubegen and be found at gaussian.com >> >>keywords>>gaussian09utilities >> >> the cubegen and formchk utilities will be the same for G03. >> >> hope this helps!! >> >> cheri >> >> 2011/2/1 =D2=F3=BD=A1 janeyin600|*|gmail.com >> >> Hello there, >>> >>> I am trying to generate a cube file with Gaussian03. However, every tim= e >>> it stops at a certain place. My command line is : >>> *# QCISD(full)/6-31G* density=3Dcurrent cube=3D(spin,coarse)* >>> with everything else and ***.cub in the end. >>> >>> And this is the ending of my output: >>> >>> Evaluate density. >>> >>> Using the spin density. >>> >>> Map the density over a grid of points, CutOff=3D 1.00D-06 >>> >>> Writing cube to file ***.cub. >>> >>> IGUnit=3D -31 Origin=3D -6.040794 -5.152992 -3.695616 >>> >>> N1=3D 72 XYZInc=3D 0.176392 0.000000 0.000000 >>> >>> N2=3D 61 XYZInc=3D 0.000000 0.176392 0.000000 >>> >>> N3=3D 42 XYZInc=3D 0.000000 0.000000 0.176392 >>> >>> I am pretty sure that it's not due to time running out and it just come= s >>> to a abrupt stop. I just wonder if anyone has the similar experience on= this >>> and a solution at hand. Thank you very much! >>> >>> Jane >>> >> >> > --000e0ce07b90651df5049b6e91cf Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: quoted-printable Hi,

I would like to mention one more thing along with Jane that don= 't change the operating system or machine for .chk file. I mean don'= ;t carry your .chk file.
After changing .chk to .fchk you can carry .fch= k file anywhere.








With regards;
 ABHISHEK SHAHI




2011/2/4 =D2=F3=BD=A1 janeyin600=3D-=3D<= a href=3D"http://gmail.com">gmail.com <owner-chemistry**ccl.net>
<= blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px= #ccc solid;padding-left:1ex;">
Yes, it works very well! I replaced "density=3Dscf" wit= h "spin=3DQCI", then I obtained the spin distribution right = away. Thank you very much, Cheri!

2011/2/1 Cheri McFerrin cmcfer1^-^tigers.lsu.edu = <owner-= chemistry/a\ccl.net>
hi jane:=20

here is what i would do.  run a single point energy using qcisd(f= ull)/6-31g*.

afterwards, run this command in order to convert your .chk file to a .= fchk file

formchk file.chk file.fchk

next, run this command to generate a .cube file

cubegen 0 density=3Dscf file.fchk 0 h

more, on formchk and cubegen and be found at gaussian.com>>keywords>>gaussian0= 9utilities

the cubegen and formchk utilities will be the same for G03.

hope this helps!!

cheri

2011/2/1 =D2=F3=BD=A1 janeyin600|*|gmail.com <owner-chemistry**= ccl.net>=20

Hello there,
 
I am trying to generate a cube file with Gaussian03. However, every ti= me it stops at a certain place. My command line is :
# QCISD(full)/6-31G* dens= ity=3Dcurrent cube=3D(spin,coarse)
with everything else and ***.cub in the end.<= /div>

And this is the ending of my output:

Evaluate density.

Using the spin density.

Map the density over a grid of points, CutOff=3D= 1.00D-06

Writing cube to file ***.cub.

IGUnit=3D -31 Origin=3D -6.040794 -5.152992 -3.6= 95616

N1=3D 72 XYZInc=3D 0.176392 0.000000 0.000000

N2=3D 61 XYZInc=3D 0.000000 0.176392 0.000000

N3=3D 42 XYZInc=3D 0.000000 0.000000 0.176392

I am pretty sure that it's not due to time r= unning out and it just comes to a abrupt stop. I just wonder if anyone has = the similar experience on this and a solution at hand. Thank= you very much!

Jane 




--000e0ce07b90651df5049b6e91cf-- From owner-chemistry@ccl.net Fri Feb 4 07:47:00 2011 From: "neha khan diya.khan.05(~)gmail.com" To: CCL Subject: CCL: problem in running configuration file using NAMD Message-Id: <-43861-110204005950-18025-Gmld92qwruuOV1dmipsWuA~~server.ccl.net> X-Original-From: "neha khan" Date: Fri, 4 Feb 2011 00:59:49 -0500 Sent to CCL by: "neha khan" [diya.khan.05~~gmail.com] Respected Sir, When i run minimization, the program stopped abnormally. What is wrong with my file? REINITIALIZING VELOCITIES AT STEP 100 TO 302 KELVIN. TCL: Running for 2500 steps ERROR: Constraint failure in RATTLE algorithm for atom 2775! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 2729! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 1739! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 2926! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 6029! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 2398! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 2202! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 3201! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 5028! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 2390! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 553! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 3136! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 4966! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 1588! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 4118! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 1275! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 771! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 1069! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 4008! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 867! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 919! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 3447! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 6355! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 4747! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 332! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 6837! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 82! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 1542! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 1254! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 9773! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 1193! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 3739! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 9465! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 953! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 10527! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 3678! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 117! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 8745! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 9881! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 10838! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 7839! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 8262! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 9955! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 10206! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 8881! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 10080! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 8404! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 8589! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 8450! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 8308! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 8580! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 8572! ERROR: Constraint failure; simulation has become unstable. ERROR: Exiting prematurely; see error messages above. ==================================================== WallClock: 74.289345 CPUTime: 74.199997 Memory: 99.713013 MB Program finished. execve failed to start process "namd2" with status: -1 execve failed to start process "namd2" with status: -1 execve failed to start process "namd2" with status: -1 execve failed to start process "namd2" with status: -1 Killed Below is my configuration file: ############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization and Equilibration of # pgl in a Water Sphere ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ../common/pgl_ws.psf coordinates ../common/pgl_ws.pdb set temperature 302 set outputname pgl_ws_eq firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../common/par_all27_prot_lipid.inp temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 13.5 # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens # Output outputName $outputname restartfreq 500 ;# 500steps = every 1ps dcdfreq 250 outputEnergies 100 outputPressure 100 ############################################################# ## EXTRA PARAMETERS ## ############################################################# # Spherical boundary conditions sphericalBC on sphericalBCcenter 30.3081743413, 28.8049907121, 15.353994423 sphericalBCr1 26.0 sphericalBCk1 10 sphericalBCexp1 2 ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization minimize 100 reinitvels $temperature run 2500 ;# 5ps From owner-chemistry@ccl.net Fri Feb 4 08:22:00 2011 From: "Sidney Ramos Santana santanasidney:_:yahoo.com.br" To: CCL Subject: CCL: Molpro execution problem in Ubuntu 10.04 Message-Id: <-43862-110204020319-6084-zfssAWCNtI9yOb/sIkYOCA..server.ccl.net> X-Original-From: "Sidney Ramos Santana" Date: Fri, 4 Feb 2011 02:03:18 -0500 Sent to CCL by: "Sidney Ramos Santana" [santanasidney||yahoo.com.br] Dear CCL Users, Please could anyone help me? I am trying to execute the Molpro 2009 in a computer with Ubuntu 10.04 64 bits (Kernel Version: 2.6.32-28 SMP, and libc6 Version: 2.11.1-0ubuntu7.8). But the program have been stopped and typed the following error: /opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe, len=50 cf3cl_8.inp, len=11 -master, len=7 ubuntu, len=6 39720, len=5 1, len=1 1, len=1 0, len=1 0, len=1 molprop_2009_1_Linux_x86_64_i8.exe: relocation error: /lib/libnss_files.so.2: symbol __r awmemchr, version GLIBC_2.2.5 not defined in file libc.so.6 with link time reference tmp = /home/sidney/pdir//opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe.p Creating: host=ubuntu, user=elizete, file=/opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe, port=39720 1: interrupt(1) Is this a Ubuntu version problem ? Please could anyone tell me what is wrong and how can I fix that ? Thanks for any help. Best Regards, Sidney R. Santana From owner-chemistry@ccl.net Fri Feb 4 10:08:00 2011 From: "Claire Coiffier claire.coiffier**univ-reims.fr" To: CCL Subject: CCL:G: problems with NBO calculation Message-Id: <-43863-110204085422-11779-zUfUj5h9O5ZahE99Nz7NbA(!)server.ccl.net> X-Original-From: "Claire Coiffier" Date: Fri, 4 Feb 2011 08:54:21 -0500 Sent to CCL by: "Claire Coiffier" [claire.coiffier*_*univ-reims.fr] Hi, I'm working on a small molecule (18 atoms: C, O, Cl and H) to study its different conformations. I'm doing a NBO calculation. I meet 2 different problems: for 2 different (but very close) conformations of the same molecule: the first calculation run successfully (ok.inp) ************************* %NPROC=12 %MEM=300MB %CHK=ok #P B3LYP 6-311++G** IOP(6/7=3) formcheck=all # POP=(FULL,esp,NBORead, SaveNLMOs) fichier a lire avec avogadro 0 1 c o 1 oc2 c 2 co3 1 coc3 c 3 cc4 2 cco4 1 dih4 c 4 cc5 3 ccc5 2 dih5 c 3 cc6 2 cco6 1 dih6 c 6 cc7 3 ccc7 2 dih7 cl 4 clc8 3 clcc8 2 dih8 cl 5 clc9 4 clcc9 3 dih9 c 1 cc10 2 cco10 3 dih10 h 3 hc11 2 hco11 1 dih11 h 4 hc12 3 hcc12 2 dih12 h 5 hc13 4 hcc13 3 dih13 h 1 hc14 2 hco14 3 dih14 h 7 hc15 6 hcc15 3 dih15 h 10 hc16 1 hcc16 2 dih16 h 10 hc17 1 hcc17 2 dih17 h 10 hc18 1 hcc18 2 dih18 oc2 1.442869 co3 1.427360 coc3 109.010 cc4 1.542390 cco4 103.069 dih4 -38.000 cc5 1.528121 ccc5 102.737 dih5 38.080 cc6 1.454824 cco6 110.587 dih6 -160.936 cc7 1.200449 ccc7 178.754 dih7 -178.193 clc8 1.801296 clcc8 112.976 dih8 160.875 clc9 1.812604 clcc9 111.671 dih9 -150.052 cc10 1.515351 cco10 108.158 dih10 149.822 hc11 1.100689 hco11 110.344 dih11 78.138 hc12 1.087702 hcc12 109.899 dih12 -80.207 hc13 1.087166 hcc13 110.555 dih13 94.077 hc14 1.098212 hco14 107.887 dih14 -92.048 hc15 1.062955 hcc15 179.771 dih15 -214.557 hc16 1.090769 hcc16 111.125 dih16 -63.345 hc17 1.091612 hcc17 110.767 dih17 175.700 hc18 1.091832 hcc18 108.753 dih18 56.331 $nbo NLMO AONLMO bndidx boao $end ************************* but the second doesn't (pb1.inp), with the following error: ************************* %NPROC=12 %MEM=300MB %CHK=pb1 #P B3LYP 6-311++G** IOP(6/7=3) formcheck=all # POP=(FULL,esp,NBORead, SaveNLMOs) fichier a lire avec avogadro 0 1 c o 1 oc2 c 2 co3 1 coc3 c 3 cc4 2 cco4 1 dih4 c 4 cc5 3 ccc5 2 dih5 c 3 cc6 2 cco6 1 dih6 c 6 cc7 3 ccc7 2 dih7 cl 4 clc8 3 clcc8 2 dih8 cl 5 clc9 4 clcc9 3 dih9 c 1 cc10 2 cco10 3 dih10 h 3 hc11 2 hco11 1 dih11 h 4 hc12 3 hcc12 2 dih12 h 5 hc13 4 hcc13 3 dih13 h 1 hc14 2 hco14 3 dih14 h 7 hc15 6 hcc15 3 dih15 h 10 hc16 1 hcc16 2 dih16 h 10 hc17 1 hcc17 2 dih17 h 10 hc18 1 hcc18 2 dih18 oc2 1.443521 co3 1.427541 coc3 109.172 cc4 1.542062 cco4 103.056 dih4 -37.540 cc5 1.527500 ccc5 102.589 dih5 38.490 cc6 1.454878 cco6 110.561 dih6 -160.476 cc7 1.200455 ccc7 178.741 dih7 -178.378 clc8 1.801069 clcc8 112.996 dih8 161.192 clc9 1.811809 clcc9 111.792 dih9 -151.187 cc10 1.515548 cco10 108.110 dih10 148.524 hc11 1.100645 hco11 110.381 dih11 78.601 hc12 1.087791 hcc12 109.940 dih12 -79.808 hc13 1.087293 hcc13 110.446 dih13 92.899 hc14 1.097943 hco14 107.905 dih14 -93.334 hc15 1.062955 hcc15 179.745 dih15 -221.111 hc16 1.090847 hcc16 111.142 dih16 -63.526 hc17 1.091585 hcc17 110.793 dih17 175.481 hc18 1.091850 hcc18 108.727 dih18 56.114 $nbo NLMO AONLMO bndidx boao $end ************************* ************************* Labels of output orbitals: RY* RY* RY* RY* RY* RY* RY* RY* RY* RY* RY* RY* Failed in SchOr1 in NBStor. Error termination via Lnk1e in /apps/gaussian/g09/l607.exe at Thu Jan 27 10:05:57 2011. ************************* I've tried both using internal coordinates and cartesian coordinates (input orientation and standard orientation), I've also tried with SCF=QC, SCF=XQC and STABLE=OPT, but the problem still remains. for the second probleme (pb2.inp), it's just a different error: ************************* %NPROC=12 %MEM=300MB %CHK=pb2 #P B3LYP 6-311++G** IOP(6/7=3) formcheck=all # POP=(FULL,esp,NBORead, SaveNLMOs) fichier a lire avec avogadro 0 1 c o 1 oc2 c 2 co3 1 coc3 c 3 cc4 2 cco4 1 dih4 c 1 cc5 2 cco5 3 dih5 c 3 cc6 2 cco6 1 dih6 c 6 cc7 3 ccc7 2 dih7 cl 4 clc8 3 clcc8 2 dih8 cl 5 clc9 1 clcc9 2 dih9 c 1 cc10 2 cco10 3 dih10 h 1 hc11 2 hco11 3 dih11 h 10 hc12 1 hcc12 2 dih12 h 10 hc13 1 hcc13 2 dih13 h 10 hc14 1 hcc14 2 dih14 h 3 hc15 2 hco15 1 dih15 h 7 hc16 6 hcc16 3 dih16 h 5 hc17 1 hcc17 2 dih17 h 4 hc18 3 hcc18 2 dih18 oc2 1.442053 co3 1.436459 coc3 110.362 cc4 1.543980 cco4 105.642 dih4 12.230 cc5 1.537725 cco5 105.335 dih5 13.068 cc6 1.455793 cco6 111.553 dih6 139.796 cc7 1.200627 ccc7 177.192 dih7 115.918 clc8 1.815751 clcc8 113.693 dih8 84.664 clc9 1.825771 clcc9 113.951 dih9 84.006 cc10 1.515677 cco10 109.921 dih10 141.411 hc11 1.097940 hco11 108.011 dih11 -99.441 hc12 1.090133 hcc12 111.121 dih12 -60.787 hc13 1.093609 hcc13 110.340 dih13 178.260 hc14 1.091500 hcc14 109.317 dih14 59.246 hc15 1.098760 hco15 108.407 dih15 -101.213 hc16 1.062823 hcc16 178.889 dih16 176.056 hc17 1.085937 hcc17 113.411 dih17 -155.002 hc18 1.085780 hcc18 112.814 dih18 -154.417 $nbo NLMO AONLMO bndidx boao $end ************************* ************************* NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO) ANALYSIS: Highest occupied NBOs are not at the beginning of the NBO list; The NLMO program is not currently set up to handle this. Illegal range for read: IUnit= 7 Address= -256 Length= -256 File length= 1894400. Error termination in NtrErr: NtrErr called from NtrIO. ************************* Once again, I've tried with internal coordinates and cartesian coordinates (input orientation and standard orientation) but nothing works. Thank you for your help From owner-chemistry@ccl.net Fri Feb 4 10:43:00 2011 From: "Victor Rosas Garcia rosas.victor*gmail.com" To: CCL Subject: CCL: dissenting results Message-Id: <-43864-110204085320-10765-HEchTXI1ow5fq8yfLINZtQ#%#server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=0015174989f6f38734049b753332 Date: Fri, 4 Feb 2011 07:53:11 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor-*-gmail.com] --0015174989f6f38734049b753332 Content-Type: text/plain; charset=ISO-8859-1 GNORM = 109.40376? That is *huge*. How did you get such a specific number, by the way? Anyway, you should be careful with the use of LET. From the manual ( http://www.openmopac.net/manual/index.html): Now LET means essentially "I know what I'm doing, override safety checks". Currently, LET has the following meanings: 1.In a FORCE calculation, it means that the supplied geometry is to be used, even if the gradients are large.So you are giving MOPAC a geometry that is not converged, and telling it to do THERMO no matter what. You could try doing the optimization using PRECISE and then do the FORCE calc without LET and GNORM. The manual is your friend! Hope this helps and have a nice day Victor 2011/2/3 Lukman Olawale Olasunkanmi waleolasunkanmi===gmail.com < owner-chemistry*ccl.net> > Thank you. > Here are typical results: > After geometry optimization without any special keyword: > FINAL HEAT OF FORMATION = 40.08240 KCAL/MOL > > With keyword "thermo", and LET GNORM = 109.40376 > > HEAT OF FORMATION = 43.366029 KCALS/MOLE > > Sometimes the difference may be up to 10kcal/mol for some calculations. > Kindly give me an advice on it. > thanks. > > > wrote: > >> >> Sent to CCL by: "Close, David M." [CLOSED!A!mail.etsu.edu] >> This is very interesting. But you need to tell us how much the numbers >> differ. I can see how sometimes very small difference could arise from >> coding errors arising from one subroutine using a double precision variable, >> and another subroutine using the same variable with a different word-length. >> But these would be very small differences. Give us an example of how big >> the differences are, and what keywords are used to control the accuracy of >> each SCF cycle. >> Regards, Dave Close. >> >> -----Original Message----- >> > From: owner-chemistry+closed==etsu.edu-$-ccl.net [mailto: >> owner-chemistry+closed ==etsu.edu-$-ccl.net] On >> Behalf Of Lukman Olawale Olasunkanm waleolasunkanmi:gmail.com >> Sent: Tuesday, February 01, 2011 8:43 AM >> To: Close, David M. >> Subject: CCL: dissenting results >> >> >> Sent to CCL by: "Lukman Olawale Olasunkanm" [waleolasunkanmi#,#gmail.com] >> Hello everyone, >> I usually run my MOPAC job twice: first for ordinary optimization from >> which I normally get the GNORM value ( and H.O.F., dipole moments, >> HOMO-LUMO, COSMOS Area and volume etc.), and second for the thermo values >> (with the specified value of the GNORM using the LET keyword). I discovered >> that the values got for the common parameters like H.O.F, dipole moments >> etc. in both cases differ. >> What can you advise me to do please? >> Thank youhttp:// >> www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>> E-mail to subscribers: CHEMISTRY-x-ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST-x-ccl.net or use>> >> >> > > > -- > *Olasunkanmi Lukman Olawale* > > *Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Nigeria.* > *+234-08052401564* > > *"Improving our own attitudes and our own state of mind takes time. Haste > and impatience can only defeat our purposes."* > > --0015174989f6f38734049b753332 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable GNORM =3D 109.40376?
=A0
That is *huge*.=A0 How did you get such a sp= ecific number, by the way?

Anyway, you should be careful with the us= e of LET.=A0 From the manual (http://www.openmopac.net/manual/index.html):

=A0=A0=A0 Now LET means essentially "I know what I'm d= oing, override safety checks".

=A0=A0=A0 Currently, LET has the following meanings:

=A0=A0=A0 1.In a FORCE calculation, it means that the supplied geometry is= to be used, even if the gradients are large.
So you are giving MO= PAC a geometry that is not converged, and telling it to do THERMO no matter= what.=A0 You could try doing the optimization using PRECISE and then do th= e FORCE calc without LET and GNORM.

The manual is your friend!

Hope this helps and have a nice day<= br>
Victor

2011/2/3 Lukman Olawale Olasunkanmi waleolasunkanmi=3D= =3D=3Dgmail.com <owner-chemistry*ccl.net>
Thank you.
Here are typical results:
After geometry optimiz= ation without any special keyword:
FINAL HEAT OF FORMATION =3D=A0 40.08240 KCAL/MOL

With keyword "= ;thermo", and LET GNORM =3D 109.40376

HEAT OF FORMATION =3D=A0=A0=A0=A0=A0 43.366029 KCALS/MOLE

Sometimes = the difference may be up to 10kcal/mol for some calculations.
Kindly gi= ve me an advice on it.
thanks.


wrote:

Sent to CCL by: "Close, David M." [CLOSED!A!mail.etsu.edu]
This is very interesting. =A0But you need to tell us how much the numbers d= iffer. =A0I can see how sometimes very small difference could arise from co= ding errors arising from one subroutine using a double precision variable, = and another subroutine using the same variable with a different word-length= . =A0But these would be very small differences. =A0Give us an example of ho= w big the differences are, and what keywords are used to control the accura= cy of each SCF cycle.
=A0Regards, Dave Close.

-----Original Message-----
> From: owner-chemistry+closed=3D=3Detsu.edu-$-ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu-$-ccl.net] On Behalf Of Lukman Ol= awale Olasunkanm waleolasunkanmi:gmail.com
Sent: Tuesday, February 01, 2011 8:43 AM
To: Close, David M.
Subject: CCL: dissenting results


Sent to CCL by: "Lukman Olawale Olasunkanm" [waleolasunkanmi#,#gmail.com]
Hello everyone,
I usually run my MOPAC job twice: first for ordinary optimization from whic= h I normally get the GNORM value ( and H.O.F., dipole moments, HOMO-LUMO, C= OSMOS Area and volume etc.), and second for the thermo values (with the spe= cified value of the GNORM using the LET keyword). I discovered that the val= ues got for the common parameters like H.O.F, dipole moments etc. in both c= ases differ.
What can you advise me to do please?
Thank youhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.n= et/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


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Olasunkanmi Lukman O= lawale

Department = of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Nigeria.
= +234-08052401564

"Improving our own attitudes and our own state of mind ta= kes time. Haste and impatience can only defeat our purposes."


--0015174989f6f38734049b753332-- From owner-chemistry@ccl.net Fri Feb 4 11:18:00 2011 From: "Pietro Ottati pietro.ottati:-:gmail.com" To: CCL Subject: CCL: Molpro execution problem in Ubuntu 10.04 Message-Id: <-43865-110204095329-12789-WH7Wy0qVOtcaqKHrypIjew-,-server.ccl.net> X-Original-From: Pietro Ottati Content-Type: multipart/alternative; boundary=002354435cf038e46e049b760ba5 Date: Fri, 4 Feb 2011 15:53:23 +0100 MIME-Version: 1.0 Sent to CCL by: Pietro Ottati [pietro.ottati++gmail.com] --002354435cf038e46e049b760ba5 Content-Type: text/plain; charset=ISO-8859-1 I'm not an expert but do you set export LD_LIBRARY_PATH in your /etc/profile to define where is the library? check MANUAL or INSTALL or REAME file of molpro... I don't use it but it's possible that the solution... --002354435cf038e46e049b760ba5 Content-Type: text/html; charset=ISO-8859-1 I'm not an expert but do you set export LD_LIBRARY_PATH in your /etc/profile to define where is the library?

check MANUAL or INSTALL or REAME file of molpro...

I don't use it but it's possible that the solution...
 --002354435cf038e46e049b760ba5-- From owner-chemistry@ccl.net Fri Feb 4 12:12:00 2011 From: "Vincent Leroux vincent.leroux\a/loria.fr" To: CCL Subject: CCL: problem in running configuration file using NAMD Message-Id: <-43866-110204120439-7603-ndv3qeih0h67/N+8t+b8AA**server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 04 Feb 2011 18:04:30 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux---loria.fr] Hi, Look at the bottom of the parameter file. What you have been doing is: - 100 minimization steps - assign velocities for 302 K all of a sudden - 2500 steps of MD 100 steps of minimization is probably not enough, but this is not the problem. You just go straight from minimization to MD: MD is started with a random set of velocities averaged to T = 302 K, resulting in your system being literally torn apart. The RATTLE algorithm tries to compensate for abnormal bond lengths occurring at the very first MD step, but of course it fails. You should do some equilibration after minimization... The comment at the beginning of your parameter file is mistaking: it says "minimization and equilibration" and below I see the (right) comment "do langevin dynamics". Seems like this input file was messed up by careless copy-paste operations. Regards VL Le 04/02/11 06:59, neha khan diya.khan.05(~)gmail.com a écrit : > Sent to CCL by: "neha khan" [diya.khan.05~~gmail.com] > Respected Sir, > When i run minimization, the program stopped abnormally. What is wrong with my file? > > REINITIALIZING VELOCITIES AT STEP 100 TO 302 KELVIN. > TCL: Running for 2500 steps > ERROR: Constraint failure in RATTLE algorithm for atom 2775! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2729! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1739! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2926! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6029! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2398! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2202! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3201! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 5028! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2390! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 553! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3136! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4966! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1588! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4118! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1275! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 771! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1069! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4008! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 867! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 919! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3447! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6355! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4747! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 332! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6837! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 82! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1542! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1254! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9773! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1193! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3739! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9465! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 953! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10527! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3678! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 117! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8745! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9881! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10838! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 7839! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8262! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9955! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10206! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8881! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10080! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8404! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8589! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8450! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8308! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8580! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8572! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Exiting prematurely; see error messages above. > ==================================================== > > WallClock: 74.289345 CPUTime: 74.199997 Memory: 99.713013 MB > Program finished. > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > Killed > > Below is my configuration file: > > > ############################################################# > ## JOB DESCRIPTION ## > ############################################################# > > # Minimization and Equilibration of > # pgl in a Water Sphere > > > ############################################################# > ## ADJUSTABLE PARAMETERS ## > ############################################################# > > structure ../common/pgl_ws.psf > coordinates ../common/pgl_ws.pdb > > set temperature 302 > set outputname pgl_ws_eq > > firsttimestep 0 > > > ############################################################# > ## SIMULATION PARAMETERS ## > ############################################################# > > # Input > paraTypeCharmm on > parameters ../common/par_all27_prot_lipid.inp > temperature $temperature > > > # Force-Field Parameters > exclude scaled1-4 > 1-4scaling 1.0 > cutoff 12. > switching on > switchdist 10. > pairlistdist 13.5 > > > # Integrator Parameters > timestep 2.0 ;# 2fs/step > rigidBonds all ;# needed for 2fs steps > nonbondedFreq 1 > fullElectFrequency 2 > stepspercycle 10 > > > # Constant Temperature Control > langevin on ;# do langevin dynamics > langevinDamping 5 ;# damping coefficient (gamma) of 5/ps > langevinTemp $temperature > langevinHydrogen off ;# don't couple langevin bath to hydrogens > > > # Output > outputName $outputname > > restartfreq 500 ;# 500steps = every 1ps > dcdfreq 250 > outputEnergies 100 > outputPressure 100 > > > ############################################################# > ## EXTRA PARAMETERS ## > ############################################################# > > # Spherical boundary conditions > sphericalBC on > sphericalBCcenter 30.3081743413, 28.8049907121, 15.353994423 > sphericalBCr1 26.0 > sphericalBCk1 10 > sphericalBCexp1 2 > > > ############################################################# > ## EXECUTION SCRIPT ## > ############################################################# > > # Minimization > minimize 100 > reinitvels $temperature > > run 2500 ;# 5ps> > > From owner-chemistry@ccl.net Fri Feb 4 16:19:00 2011 From: "Oleg Trott trott[-]scripps.edu" To: CCL Subject: CCL: Announcement: web interface for performing virtual screening Message-Id: <-43867-110204161611-21180-r8LTHNWz8Xpd1vUHsYy0Fw/./server.ccl.net> X-Original-From: Oleg Trott Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 4 Feb 2011 13:15:56 -0800 MIME-Version: 1.0 Sent to CCL by: Oleg Trott [trott++scripps.edu] Dear Colleagues, On behalf of the Watowich lab at the University of Texas Medical Branch, I am excited to announce the availability of a web-driven interface for performing structure-based virtual screening with AutoDock Vina: http://docking.utmb.edu/ Please don't miss the FAQ linked from the main web site, and a comparison against the DUD benchmark: http://docking.utmb.edu/dudresults/ Cheers, Oleg -- Oleg Trott, Ph.D. (Columbia University) Staff Scientist in the Olson Lab The Scripps Research Institute http://olegtrott.com From owner-chemistry@ccl.net Fri Feb 4 16:53:00 2011 From: "David Neil Bowman dnbowman|a|ncsu.edu" To: CCL Subject: CCL: Restarting TDDFT calculation in ORCA 2.8 Message-Id: <-43868-110204145850-27133-RSfF1FVInX/bKweCTc2DOA:+:server.ccl.net> X-Original-From: "David Neil Bowman" Date: Fri, 4 Feb 2011 14:58:49 -0500 Sent to CCL by: "David Neil Bowman" [dnbowman(0)ncsu.edu] Is it possible to restart an ORCA TDDFT calculation from where the program halted (time limit restrictions forced this) or from a completed calculation with fewer roots? Currently I have only been able to restart with Guess=MORead and MOInp="myfile.gbw" options from the initial optimization calculation. David Bowman Graduate Student North Carolina State University, Chemistry Department From owner-chemistry@ccl.net Fri Feb 4 17:28:00 2011 From: "Kirk Peterson kipeters_._wsu.edu" To: CCL Subject: CCL: Molpro execution problem in Ubuntu 10.04 Message-Id: <-43869-110204103326-22702-M3wTSdQeb4nERTqA4i74Pg*server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 4 Feb 2011 07:33:17 -0800 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Kirk Peterson [kipeters .. wsu.edu] Dear Sidney, looks like an installation problem. Do the test jobs work? Which compiler are you using? I would strongly recommend to post this to the Molpro users list (molpro-user at molpro.net). You'll certainly get this worked out there. regards, -Kirk On Feb 3, 2011, at 11:03 PM, Sidney Ramos Santana santanasidney:_:yahoo.com.br wrote: > > Sent to CCL by: "Sidney Ramos Santana" [santanasidney||yahoo.com.br] > Dear CCL Users, > > Please could anyone help me? > > I am trying to execute the Molpro 2009 in a computer with > > Ubuntu 10.04 64 bits (Kernel Version: 2.6.32-28 SMP, and > > libc6 Version: 2.11.1-0ubuntu7.8). > > But the program have been stopped > > and typed the following error: > > /opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe, len=50 > cf3cl_8.inp, len=11 > -master, len=7 > ubuntu, len=6 > 39720, len=5 > 1, len=1 > 1, len=1 > 0, len=1 > 0, len=1 > molprop_2009_1_Linux_x86_64_i8.exe: relocation error: /lib/libnss_files.so.2: > symbol __r awmemchr, version GLIBC_2.2.5 not defined in file libc.so.6 with > link time reference > tmp = /home/sidney/pdir//opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe.p > Creating: host=ubuntu, user=elizete, > file=/opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe, port=39720 > 1: interrupt(1) > > Is this a Ubuntu version problem ? > > Please could anyone tell me what is wrong and how can I fix that ? > > Thanks for any help. > > Best Regards, > > Sidney R. Santana> > From owner-chemistry@ccl.net Fri Feb 4 18:08:00 2011 From: "Edroaldo Lummertz da Rocha edroaldo()gmail.com" To: CCL Subject: CCL: Truncated octahedron Message-Id: <-43870-110204162944-16407-SlvpKfEwnKb78QfOjvV/1Q:server.ccl.net> X-Original-From: Edroaldo Lummertz da Rocha Content-Type: multipart/alternative; boundary=00504502daac725fbb049b7b9240 Date: Fri, 4 Feb 2011 19:29:07 -0200 MIME-Version: 1.0 Sent to CCL by: Edroaldo Lummertz da Rocha [edroaldo:_:gmail.com] --00504502daac725fbb049b7b9240 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks so much. All answers are very good and useful. Thanks. Beste regards, Edroaldo 2011/2/3 Mihaly Mezei Mihaly.Mezei]*[mssm.edu > > Sent to CCL by: Mihaly Mezei [Mihaly.Mezei-*-mssm.edu] > > > > > Sent to CCL by: "Edroaldo Lummertz da Rocha" [edroaldo:_:gmail.com] > > Hi, I am starting to construct models to use in molecular dynamics > > simulations and I can not find information about how build atomistic > > nanoparticles and nanomaterials models. For example, I need to model a > > truncated octahedron gold nanoparticle. What is the methodology > > for that? > > My program Simulaid (http://inka.mssm.edu/~mezei/simulaid) > can trim a set of atoms/molecules to be contained withi a number of perio= dic > cell shapes, including truncated octehedron. It can also print a PDB file > with the vertices of these shapes for easy visualization. > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of > Medicine > Voice: (212) 659-5475 Fax: (212) 849-2456 > WWW (MSSM home): > http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=3D000007250000= 1497192632 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > WWW (Department): http://atlas.physbio.mssm.edu > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Edroaldo Lummertz da Rocha Doutorando em Ci=EAncia e Engenharia de Materiais GruDE - EEL - CTC - UFSC Phn. ---- http://www.grude.ufsc.br Mude Sua Vida, Mude o Mundo --00504502daac725fbb049b7b9240 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks so much. All answers are very good and useful. Thanks.

Beste = regards, Edroaldo

2011/2/3 Mihaly Mezei M= ihaly.Mezei]*[mssm.edu &l= t;owner-chemistry:+:ccl.net>= ;

Sent to CCL by: Mihaly Mezei [Mihaly.Mezei-*-mssm.edu]



> Sent to CCL by: "Edroaldo Lummertz =A0da Rocha" [edroaldo:_:= gmail.com]
> Hi, I am starting to construct models to use in molecular dynamics
> simulations and I can not find information about how build atomistic > nanoparticles and nanomaterials models. For example, I need to model a=
> truncated octahedron gold nanoparticle. What is the methodology
> for that?

My program Simulaid (http://inka.mssm.edu/~mezei/simulaid) can trim a set of = atoms/molecules to be contained withi a number of periodic cell shapes, inc= luding truncated octehedron. It can also print a PDB file with the vertices= of these shapes for easy visualization.

Mihaly Mezei

Department of Structural and Chemical Biology, Mount Sinai School of Medici= ne
Voice: =A0(212) 659-5475 =A0 Fax: (212) 849-2456
WWW (MSSM home): http://www.mountsin= ai.org/Find%20A%20Faculty/profile.do?id=3D0000072500001497192632
WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
WWW (Department): http://atlas.physbio.mssm.edu



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY:+:ccl.n= et or use:
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--
Edroaldo Lummertz da Ro= cha
Doutorando em Ci=EAncia e Engenharia de Materiais
GruDE - EEL - C= TC - UFSC
Phn. ----
http://www.grude.ufsc.br
Mude Sua Vida, Mude o Mundo
--00504502daac725fbb049b7b9240-- From owner-chemistry@ccl.net Fri Feb 4 19:05:01 2011 From: "David Gallagher gallagher.da]|[gmail.com" To: CCL Subject: CCL: MOPAC and metals Message-Id: <-43871-110204190313-13069-j4/kCW3ZZPy7I9aAJqu87w%%server.ccl.net> X-Original-From: David Gallagher Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Fri, 04 Feb 2011 16:02:26 -0800 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da],[gmail.com] Hi Jose, What you are asking is certainly possible when optimizing with molecular mechanics methods, however, with quantum methods such as MOPAC, the only things you can really control are the starting positions of the atoms, the number of electrons (net charge), and the multiplicity (although, it is possible to lock atom positions, bond lengths, angles and dihedrals). Even the bonds you see on the screen are ignored by a quantum mechanics program. Once the optimization is complete, MOPAC decides where the electrons should go and so effectively controls the bonding, partial charges and oxidation states. Do not be misled by some graphical representations of the bonding, but look at the final atom distances, calculated bond orders, partial changes, and molecular orbitals, etc. Regarding adding counter ions, this is usually fine. Also, unless you are simulating gas phase, you should use the appropriate solvent field (e.g. COSMO) or explicit solvent molecules, particularly when there are charged or polar species present. David Gallagher CAChe Research.com At 04:34 AM 2/2/2011, Jose Goncalo Deira Duarte de Campos Justino jgcj|fct.unl.pt wrote: >Sent to CCL by: "Jose Goncalo Deira Duarte de >Campos Justino" [jgcj:_:fct.unl.pt] >Dear all, > >I've been thinking about using mopac2009 to model some iron-porphyrin >systems. The aim so far is to check how the software behaves. I'm quite >familiar with mopac by now, but the metal atom has been triggering some >questions. > >Formally, I have an iron (IV) atom complexed equatorially by the 4 N atoms > > from porphyrin (which has a radical cation delocalized over the aromatic >part and two anionic carboxylate groups) and, apically, by a HS- >(thiolate) group and an O atom (formal charge -2). This should be neutral. >(for those of you who might recognize, it's derived from the P450 compound >I active site). > >Playing with mopac and mozyme and related keywords from the manual, I >never get a Fe(IV) state but a Fe(II) state. Is there anyway to set this >in the input file? > >My best try so far got me a total charge of -3 with very good geometries, >so i threw in 3 K+ atoms, and the geometry remained excellent. What do you >feel about the validity of this approach ? > >Paralell, is there any particular way to specify dative bonds in mopac >such as those of Fe to the porphyrin N atoms ? Is SETPI the best option >for these, or totally non-sense ? > >Any input (any at all, really) is welcome! > >All the best, >Gonçalo From owner-chemistry@ccl.net Fri Feb 4 22:49:00 2011 From: "dhacademic dhacademic---gmail.com" To: CCL Subject: CCL:G: generate electrostatic potential map problem in Gaussian Message-Id: <-43872-110204223723-18803-IhCkAlT4jLoABb9QFowPwg###server.ccl.net> X-Original-From: dhacademic Content-Type: multipart/alternative; boundary=20cf30433fa4fa95a5049b80b660 Date: Fri, 4 Feb 2011 22:37:14 -0500 MIME-Version: 1.0 Sent to CCL by: dhacademic [dhacademic[a]gmail.com] --20cf30433fa4fa95a5049b80b660 Content-Type: text/plain; charset=ISO-8859-1 Hi Everyone, I experience a problem in generating electrostatic potential map with Gaussian calculation. I have tried small molecules (2 water molecules). After single point calculation, the "Total Density" type of cube can be generated in "GView 3 -- Results -- Surface -- Cube action" with fchk file. Then with this cube, the "ESP type" new mapped surface can be generated in "surface action", which is what I expect. But for a relative larger system (about 20 atoms), in the "cube action" step, an error message appears: "surface build failed. No data to plot. Isovalue my be out of range." So I tried cubegen to generate potential cube file from fchk file. Then the following error message appears: PGFIO-F-231/formatted read/unit=20/error on data conversion. File name = 3lbw-DP-DoD1-NMR-fullQM.fchk formatted, sequential access record = 297544 In source file fchkrd.f, at line number 41 I have the following questions: (1) why the electrostatic potential surface need to be generated based on "total density" type of cube instead of "ESP" type of cube? I also tried the latter cube, but a strange surface can be obtained. (2) Is there any additional keyword needed in the root section of gaussian calculation for ESP calculation? (3) I do not understand why only ESP of small molecule (< 10 atoms) can be generated? And why I fail in medium size system? Is there any atom size limitation for cubegen in both g03 and g09? My friend and I tried both version, but neither of them can generate potential cube file from fchk file. The command we used is "cubegen 0 potential a.fchk a_pot.cube 80" Any suggestion is appreciated! Best, Hao --20cf30433fa4fa95a5049b80b660 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Everyone,

I experience a problem in generating electrostatic pote= ntial map with Gaussian calculation. I have tried small molecules (2 water = molecules). After single point calculation, the "Total Density" t= ype of cube can be generated in "GView 3 -- Results -- Surface -- Cube= action" with fchk file. Then with this cube, the "ESP type"= new mapped surface can be generated in "surface action", which i= s what I expect.

But for a relative larger system (about 20 atoms), in the "cube ac= tion" step, an error message appears:
"surface build failed. <= br>No data to plot.
Isovalue my be out of range."

So I tri= ed cubegen to generate potential cube file from fchk file. Then the followi= ng error message appears:

PGFIO-F-231/formatted read/unit=3D20/error on data conversion.
File = name =3D 3lbw-DP-DoD1-NMR-fullQM.fchk=A0=A0=A0 formatted, sequential
ac= cess=A0=A0 record =3D 297544
In source file fchkrd.f, at line number 41<= br>
I have the following questions:
(1) why the electrostatic potential surface need to be generated based on &= quot;total density" type of cube instead of "ESP" type of cu= be? I also tried the latter cube, but a strange surface can be obtained.
(2) Is there any additional keyword needed in the root section of gauss= ian calculation for ESP calculation?

(3) I do not understand why onl= y ESP of small molecule (< 10 atoms) can be generated? And why I fail in= medium size system? Is there any atom size limitation for cubegen in both = g03 and g09? My friend and I tried both version, but neither of them can ge= nerate potential cube file from fchk file. The command we used is "cub= egen 0 potential a.fchk a_pot.cube 80"
=A0
Any suggestion is appreciated!

Best,
Hao
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