From owner-chemistry@ccl.net Sat Feb 18 00:05:00 2006 From: "HAO JIANG jianghao:_:pitt.edu" To: CCL Subject: CCL: Help on Molecular Dynamics software Message-Id: <-30921-060217191914-21170-NK+jWiLzp6FPpA6KxcGD1Q###server.ccl.net> X-Original-From: "HAO JIANG" Date: Fri, 17 Feb 2006 19:19:13 -0500 Sent to CCL by: "HAO JIANG" [jianghao..pitt.edu] Does anyone know a good parallel Molecular Dynamics code that can handle polarizable force field such as Dang-Chang or AMOEBA? I am currently using TINKER, which is a very good package, but the code is not paralleled. I also have a question about making movies from TINKER trajectory files. I know that ForceFieldExploer of TINKER can display the trajectory, but I don't know how to save the trajectory animation in other format that is replayable in, say, Microsoft PowerPoint presentations. Any suggestion is greatly appreciated. Hao Jiang Department of Chemistry University of Pittsburgh From owner-chemistry@ccl.net Sat Feb 18 05:26:00 2006 From: "Mgr. Lubos Vrbka lubos.vrbka-,-uochb.cas.cz" To: CCL Subject: CCL: Help on Molecular Dynamics software Message-Id: <-30922-060218051531-14775-8jiVtsqljuZtRc5Gs2Jbrw:-:server.ccl.net> X-Original-From: "Mgr. Lubos Vrbka" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Sat, 18 Feb 2006 11:15:29 +0100 MIME-Version: 1.0 Sent to CCL by: "Mgr. Lubos Vrbka" [lubos.vrbka()uochb.cas.cz] hi, > Does anyone know a good parallel Molecular Dynamics code that can handle polarizable force field such as Dang-Chang or AMOEBA? I am currently using TINKER, which is a very good package, but the code is not paralleled. afaik, amoeba is supported only in tinker. example of parallel codes include gromacs, namd, dlpoly... you'll have to check whether they support what you need. > I also have a question about making movies from TINKER trajectory files. I know that ForceFieldExploer of TINKER can display the trajectory, but I don't know how to save the trajectory animation in other format that is replayable in, say, Microsoft PowerPoint presentations. isn't it possible to read the trajectory to vmd? the movie plugin in vmd is capable of creating mpeg files that should be possible to include in powerpoint presentations. in the past, when i worked with tinker, i used gopenmmol for visualization and graphics/movies, so maybe you could give it a try. regards, lubos -- ..................................................... Mgr. Lubos Vrbka Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic http://www.molecular.cz/~vrbka ..................................................... From owner-chemistry@ccl.net Sat Feb 18 10:11:00 2006 From: "Dharani dharan Mudaliar biodharani.:.yahoo.co.in" To: CCL Subject: CCL: Autodock download from browsers Message-Id: <-30923-060217121437-17649-QO7nW/TN2E2pZaIukKysoQ^^server.ccl.net> X-Original-From: "Dharani dharan Mudaliar" Date: Fri, 17 Feb 2006 12:14:36 -0500 Sent to CCL by: "Dharani dharan Mudaliar" [biodharani*yahoo.co.in] Hi to all!!!! i am a biotech student from india, i am doing a project in docking molecules,i could not down load AUTDOCK TOOL ,my PC is working on windows xp OS, Those who have already worked in autodock put ur suggeestions in downloading,compiling AUTODOCK. Thank u friends sincerely dharani From owner-chemistry@ccl.net Sat Feb 18 10:59:01 2006 From: "Richard M. Casey rcasey::rmcbiosciences.com" To: CCL Subject: CCL: ECCE and molecular dynamics Message-Id: <-30924-060218105556-2819-9N2ibROBQDE+5nCBqjQjIg(-)server.ccl.net> X-Original-From: "Richard M. Casey" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0008_01C63461.ECDA2830" Date: Sat, 18 Feb 2006 08:04:21 -0700 MIME-Version: 1.0 Sent to CCL by: "Richard M. Casey" [rcasey- -rmcbiosciences.com] This is a multi-part message in MIME format. ------=_NextPart_000_0008_01C63461.ECDA2830 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable CCL'ers, Is this an appropriate listserv to send questions about ECCE, the = graphical front-end for NWCHEM? If not, is there another listserv more = appropriate for ECCE? Otherwise, we're trying to set up a molecular = dynamics simulation using ECCE but cannot get through the right sequence = of steps based on the documentation. If anyone has a simple example of = how to use ECCE to setup and run MD simulations, it would be most = appreciated. =20 Regards, Richard Casey ------=_NextPart_000_0008_01C63461.ECDA2830 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
CCL'ers,
 
Is this an appropriate listserv to send = questions=20 about ECCE, the graphical front-end for NWCHEM?  If not, is there = another=20 listserv more appropriate for ECCE?  Otherwise, we're trying to set = up a=20 molecular dynamics simulation using ECCE but cannot get through the = right=20 sequence of steps based on the documentation.  If anyone has a = simple=20 example of how to use ECCE to setup and run MD simulations, it would be = most=20 appreciated.
 
 
Regards,
Richard = Casey
------=_NextPart_000_0008_01C63461.ECDA2830-- From owner-chemistry@ccl.net Sat Feb 18 15:43:01 2006 From: "zborowsk]![chemia.uj.edu.pl" To: CCL Subject: CCL:G: Problem with Frequency Calculation Gaussian 03 Message-Id: <-30925-060218060112-4505-T/6bT15aNc7hY934OAfC/A+*+server.ccl.net> X-Original-From: zborowsk===chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Sat, 18 Feb 2006 11:16:14 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: zborowsk__chemia.uj.edu.pl Hi I do not know what crashed but your mail generate more general question. Namely, after reading of your letter I not sure. Have you obtained full optimized geometrical structure of your cluster or not??? If not, where is the sence of performing vibrational analysis? regards > Sent to CCL by: "Adrian Villlegas" [adriano-$-eps.mcgill.ca] > Hello everyone, > I was wondering if anybody can provide some help on the way to perform > succesfully a frequency calculation using Gaussian 03. > I have tried several times to run a frequency calculation (on a Pentium IV > machine) of a succesfully optimized ionrganic cluster - > Hartree-Fock-6-31G(d,p)- involving 50 atoms. The geometry optimization > required the use of the "modredundant" function in order to freeze some of > the atoms in the cluster. > I have run the frequency calculation in two modes: i) inlcuding the > modredundant function as in I did in the geometry optimisatin and ii) by > unlocking all atoms in the cluster (modredundant option not considered), > in both cases I used the same basis set as used for the geometry > optimization: 6-31G(d,p). Thus far, the calculation runs until a point > where the program crashes and a: "severe error message 2070" is displayed > Below I have copy-pasted the last section of the incompleted calculation > as displayed in the output file: > > > The electronic state of the initial guess is 1-A. > Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. > Requested convergence on MAX density matrix=1.00D-06. > Requested convergence on energy=1.00D-06. > No special actions if energy rises. > Restarting incremental Fock formation. > SCF Done: E(RHF) = -8605.99834357 A.U. after 21 cycles > Convg = 0.5842D-08 -V/T = 2.0012 > S**2 = 0.0000 > Range of M.O.s used for correlation: 1 797 > NBasis= 797 NAE= 235 NBE= 235 NFC= 0 NFV= 0 > NROrb= 797 NOA= 235 NOB= 235 NVA= 562 NVB= 562 > Differentiating once with respect to electric field. > with respect to dipole field. > Electric field/nuclear overlap derivatives assumed to be zero. > Integrals replicated using symmetry in FoFDir. > MinBra= 0 MaxBra= 2 Meth= 1. > IRaf= 0 NMat= 3 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 2 > JSym2E=2. > There are 3 degrees of freedom in the 1st order CPHF. > 3 vectors were produced by pass 0. > AX will form 3 AO Fock derivatives at one time. > 3 vectors were produced by pass 1. > 3 vectors were produced by pass 2. > 3 vectors were produced by pass 3. > 3 vectors were produced by pass 4. > 3 vectors were produced by pass 5. > 3 vectors were produced by pass 6. > 3 vectors were produced by pass 7. > 3 vectors were produced by pass 8. > 3 vectors were produced by pass 9. > 3 vectors were produced by pass 10. > 3 vectors were produced by pass 11. > 3 vectors were produced by pass 12. > 3 vectors were produced by pass 13. > 3 vectors were produced by pass 14. > 3 vectors were produced by pass 15. > 3 vectors were produced by pass 16. > 3 vectors were produced by pass 17. > Inv2: IOpt= 1 Iter= 1 AM= 3.15D-15 Conv= 1.00D-12. > Inverted reduced A of dimension 54 with in-core refinement. > End of Minotr Frequency-dependent properties file 721 does not exist. > Symmetrizing basis deriv contribution to polar: > IMax=3 JMax=2 DiffMx= 0.00D+00 > G2DrvN: will do 18 centers at a time, making 3 passes doing > MaxLOS=2. > FoFDir/FoFCou used for L=0 through L=2. > Differentiating once with respect to electric field. > with respect to dipole field. > Differentiating once with respect to nuclear coordinates. > Integrals replicated using symmetry in FoFDir. > MinBra= 0 MaxBra= 2 Meth= 1. > IRaf= 0 NMat= 52 IRICut= 52 DoRegI=T DoRafI=T ISym2E= 2 > JSym2E=2. > Raff turned off since only 49.75% of shell-pairs survive. > There are 156 degrees of freedom in the 1st order CPHF. > 153 vectors were produced by pass 0. > AX will form 51 AO Fock derivatives at one time. > 153 vectors were produced by pass 1. > writwa > > > Thanks a lot for your feedback > > Adrin> > > > -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk,chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70