Hi Dave,
thanks for your reply!!

I'm using Gaussian09 and my = system is really small, I'm doing a test with one Pd(II) atom in square pla= nar stereo-chemistry with two H2O molecules and two OH- groups as ligands i= nteracting with one H2 molecule.
---------------------------------------= ---------------------------------------------------------------------------= --
118 basis functions, 217 primitive gaussians= , 124 cartesian basis functions
29 alpha = electrons 29 beta electrons
--------= ---------------------------------------------------------------------------= --------------------------------
Previously I did one MP2 optimization o= f the system (without counterpoise) with no problems. So I don't believe that the Error is related with storage capacity (actually, I have done cal= culation on bigger systems with more than 300 basis functions). I speculate= that It seems to be related with the reading of some file or keyword when = the second step starts.

I forgot to mention that in this particular = case the Pd cluster is fixed (opt=3Dz-matrix) an the optimization is only d= one on the H2 coordinates.

However I have not tried that option (%rw= f), I'll give a look...

Thanks again..

Diego
=0AUPV-ITQ
= =0ASpain.

=0A=0A

<= br>

From: "Close, David M. CLOSED_._= mail.etsu.edu" <owner-chemistry%x%ccl.net>
To: "Gomez, Diego Armando " <darkego21%x%y= ahoo.com>
Sent: Thu,= April 22, 2010 8:02:19 PM
Subject= : CCL: Error termination in NtrErr at MP2 calculation.

=0A=0A=0A=0A =0A =0A= =0A=0A=0A=0A

=0A=0A

Diegoi:

=0A=0A

This is a common error that means you have exceeded disc storage= =0Aspace. This happens with MP2 calculations that requires a great de= al of=0Ascratch disc space for storing integrals. There are common fi= xes to this=0Aproblem, but it is necessary to tell us about the size of the= calculation you=0Aare doing. Like how many heavy atoms, and what pro= gram you are=0Ausing. Basically a 32 bit machine is limited to 16 Gby= tes of storage. =0AHave you tried simple fixes like %rwf=3D = ; =E2=80=A6. ?

=0A=0A

= Regards, Dave Close.

=0A=0A

= =0A=0A

From:=0Aowner-chemistry+closed=3D=3Detsu.e= du*ccl.net=0A[mailto:owner-chemistry+closed=3D=3Detsu.edu*ccl.net] On Be= half Of DIEGOI=0AGOMEZ darkego21 ~ yahoo.com
=0ASent: Thursday, April 22, 2010 9:56 A= M
=0ATo: Close, David M.
=0ASubject: CCL: Error termina= tion in NtrErr at MP2 calculation.

=0A=0A

=0A= =0A

=0A=0A

Hello there.
=0A
=0AI'm do= ing an optimization of a pair of interacting molecules at MP2 level with=0A= simultaneous counterpoise correction. I'm using two basis set (lanl2dz and= =0A6-31G**) through the "GEN" keyword. The calculation starts=0Awitho= ut problems, so the first SCF cycle and the second-order perturbation are= =0Aaccomplished. However, when the next step starts the follow Error is rep= orted:
=0A
=0A-------------------------------------------------------= ---------------------------------------------------------------------------= -----------
=0A ***** Axes restored to original set *****
=0A&n= bsp;Cartesian Forces: Max     0.199455160=0ARMS&n= bsp;    0.055013514
=0A Operation on file out of ran= ge.
=0AFileIO: IOper=3D 2 IFilNo(1)=3D -522=0ALen=3D  &n= bsp;      118=0AIPos=3D    &nb= sp;    118 Q=3D  =0A47965310131088
=0A
=0A=0A dumping /fiocom/, unit =3D 1 NFiles =3D    98 Siz= Ext=0A=3D    524288 WInBlk =3D     = 512
=0A         &nbs= p;        =0Adefal =3D T LstWrd =3D=    233431552 FType=3D2 FMxFil=3D10000
=0A
=0A Number&n= bsp;         =0A0  &= nbsp;      =0A0     =     =0A0        = ; 0         =0A0 &n= bsp;       =0A0    &= nbsp;    =0A0       =    0
=0A Base      12203972 = ;   =0A390144     495616  &nbs= p; =0A321536   12752384   10698752  &nbs= p; =0A201216     365568
=0A End  = ;     12204032    =0A402432 &n= bsp;   527360    =0A322048   128189= 44   11614208    =0A201728   &= nbsp; 372736
=0A End1      12204032 &= nbsp;  =0A402432     527360   = =0A322048   12818944   11614208   = 201728    =0A372736
=0A Wr Pntr &nb= sp; 12203972    =0A388608     49561= 6    =0A321536   12533760   1069875= 2    =0A201216     365568
=0A&nb= sp;Rd Pntr   12203972    =0A388608  = ;   495616    =0A321536   12533760&= nbsp; 10698752    =0A201216   &nbs= p; 365568
=0A Length        = ; =0A60      12288    &nb= sp;=0A31744       =0A512  &nbs= p;   66560    =0A915456   &nbs= p;   =0A512       7168
=0A<= br>=0A(...)

=0A=0A

Error termination in=0ANtrErr:
=0A&nbs= p;NtrErr Called from FileIO.
=0A
=0A---------------------------------= ---------------------------------------------------------------------------= ----------------------------------
=0A
=0AThanks in advance for any s= ugestion.
=0A
=0ADiego
=0AUPV-ITQ
=0ASpain.

=0A=0A=0A=0A

=0A=0A

=0A=0A=

=0A

=0A=0A --0-888992762-1271967861=:48501-- From owner-chemistry@ccl.net Fri Apr 23 11:40:00 2010 From: "Wendy Warr wendy[*]warr.com" To: CCL Subject: CCL: InChI Trust RFP for InChi/InChiKey Certification & Testing Message-Id: <-41707-100423102850-27662-w+dTjz201F7JN2S6XgtaRw*|*server.ccl.net> X-Original-From: "Wendy Warr" Date: Fri, 23 Apr 2010 10:28:49 -0400 Sent to CCL by: "Wendy Warr" [wendy_._warr.com] Posted on behalf of Steve Heller: The InChI Trust http://www.inchi-trust.org wishes to contract for a system that will provide for certification and testing of the InChI/InChiKey algorithm. Persons/organizations who wish to consider bidding on this contract can request a copy of the RFP from: steve- -inchi-trust.org From owner-chemistry@ccl.net Fri Apr 23 12:14:00 2010 From: "Jim Kress ccl_nospam^^kressworks.com" To: CCL Subject: CCL: TINKER sovation with polar molecules Message-Id: <-41708-100423113946-4989-7WkurxNLOk0pQmSFRb52Yg##server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 23 Apr 2010 11:39:29 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam- -kressworks.com] Try gromacs http://www.gromacs.org/ For MD it is faster than Tinker, easier to use, runs in parallel, and supports just as many classical force fields - along with a variety of multiple time scale (and other) methods not available in Tinker. It also provides a much larger set of tools to analyze and interpret your results. The same could be said for LAMMPS http://lammps.sandia.gov/ with the additional comment that classical AND REACTIVE force fields are also supported (e.g. REAXFF). Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com . ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com . ccl.net] On Behalf Of Kelly 8D > i.m.smilin.kelly]_[gmail.com > Sent: Thursday, April 22, 2010 2:09 PM > To: Kress, Jim > Subject: CCL: TINKER sovation with polar molecules > > Hi CCL users! > > I am trying to solvate a small molecule in water using TINKER. I have searched the > archives, and found references to xyzedit and soak. I don't have soak, so am using > xyzedit. > > When generating the water with xyzedit (option 16), the water box contains water > molecules that are all aligned in the same direction. So when I try to minimize, > optimize, or Newton the xyz file, to relax it into something i can do MD on, the > program crashes with: > > > INDUCE -- Warning, Induced Dipoles are not Converged > > TINKER is Unable to Continue; Terminating the Current Calculation > > > I find that small systems (~<30 waters) will run - probably because the system as a > whole has less dipole moment - but I know most users are making bigger boxes > than that... > > How are you relaxing the system enough to do MD? > > > If you prefer to reply in person, e-mail is kelly.theel=email.ucr.edu > > Thanks for any help you can give! > > -- > - Kelly > > "Most folks are about as happy as they make up their minds to be." - Abraham > Lincoln From owner-chemistry@ccl.net Fri Apr 23 18:39:00 2010 From: "Albert Poater albertpo##stark.udg.es" To: CCL Subject: CCL:G: Linux vs Windows Message-Id: <-41709-100423084954-12791-7/2Bp5XoFy4in1SXN2ckIg- -server.ccl.net> X-Original-From: "Albert Poater" Date: Fri, 23 Apr 2010 08:49:52 -0400 Sent to CCL by: "Albert Poater" [albertpo^-^stark.udg.es] Dear CCL users, Does anybody any experience with the performance of Gaussian with the Window platform (not XP, I mean the professional version that does not contain graphical applications)? I am pretty sure that the performance is much slower with respect to Linux but which is the percentage and the main doubt is if Windows is stable or not tu run Gaussian. Which is the performance for clusters with blades with nodes of two QUAD-cores? Thanks in advance, Albert From owner-chemistry@ccl.net Fri Apr 23 20:02:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim|compchem.net" To: CCL Subject: CCL:G: Error termination in NtrErr at MP2 calculation. Message-Id: <-41710-100423181523-28073-SlvpKfEwnKb78QfOjvV/1Q],[server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=00163642652302bce30484ee5205 Date: Fri, 23 Apr 2010 22:43:39 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim{}compchem.net] --00163642652302bce30484ee5205 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Diego I read your complain about a NtrErr error. This type of errors happens in different cases, one of them as Dave mentioned due to space issue, and in this case NMax information should be mentioned in last few lines, which is not available in the supported information you gave. Another possibility is the checkpoint file, what happened is your checkpoint file has not be created, or optimization data (for first cycle) has not be saved in your checkpoint file. that is what you have got. There is no technical solve for this error. Just, try to build up your inpu= t file again, save checkpoint file (%chk=3Dfilename.chk) and change its path. If you got the error again, you would send your input file and we can test it. Sincerely; M. Ibrahim On Thu, Apr 22, 2010 at 9:24 PM, DIEGOI GOMEZ darkego21]_[yahoo.com < owner-chemistry^-^ccl.net> wrote: > Hi Dave, > thanks for your reply!! > > I'm using Gaussian09 and my system is really small, I'm doing a test with > one Pd(II) atom in square planar stereo-chemistry with two H2O molecules = and > two OH- groups as ligands interacting with one H2 molecule. > > -------------------------------------------------------------------------= ------------------------------------------- > 118 basis functions, 217 primitive gaussians, 124 cartesian basis > functions > 29 alpha electrons 29 beta electrons > > -------------------------------------------------------------------------= ------------------------------------------ > Previously I did one MP2 optimization of the system (without counterpoise= ) > with no problems. So I don't believe that the Error is related with stora= ge > capacity (actually, I have done calculation on bigger systems with more t= han > 300 basis functions). I speculate that It seems to be related with the > reading of some file or keyword when the second step starts. > > I forgot to mention that in this particular case the Pd cluster is fixed > (opt=3Dz-matrix) an the optimization is only done on the H2 coordinates. > > However I have not tried that option (%rwf), I'll give a look... > > Thanks again.. > > Diego > UPV-ITQ > Spain. > > > > > ------------------------------ > *From:* "Close, David M. CLOSED_._mail.etsu.edu" ccl.net> > *To:* "Gomez, Diego Armando " > *Sent:* Thu, April 22, 2010 8:02:19 PM > *Subject:* CCL: Error termination in NtrErr at MP2 calculation. > > Diegoi: > > This is a common error that means you have exceeded disc storage space. > This happens with MP2 calculations that requires a great deal of scratch > disc space for storing integrals. There are common fixes to this problem= , > but it is necessary to tell us about the size of the calculation you are > doing. Like how many heavy atoms, and what program you are using. > Basically a 32 bit machine is limited to 16 Gbytes of storage. Have you > tried simple fixes like %rwf=3D =85. ? > > Regards, Dave Close. > > > > *From:* owner-chemistry+closed=3D=3Detsu.edu*ccl.net [mailto: > owner-chemistry+closed =3D=3Detsu.edu*ccl.net] = *On > Behalf Of *DIEGOI GOMEZ darkego21 ~ yahoo.com > *Sent:* Thursday, April 22, 2010 9:56 AM > *To:* Close, David M. > *Subject:* CCL: Error termination in NtrErr at MP2 calculation. > > > > Hello there. > > I'm doing an optimization of a pair of interacting molecules at MP2 level > with simultaneous counterpoise correction. I'm using two basis set (lanl2= dz > and 6-31G**) through the "GEN" keyword. The calculation starts without > problems, so the first SCF cycle and the second-order perturbation are > accomplished. However, when the next step starts the follow Error is > reported: > > > -------------------------------------------------------------------------= -------------------------------------------------------------------- > ***** Axes restored to original set ***** > Cartesian Forces: Max 0.199455160 RMS 0.055013514 > Operation on file out of range. > FileIO: IOper=3D 2 IFilNo(1)=3D -522 Len=3D 118 IPos=3D = 118 Q=3D > 47965310131088 > > > dumping /fiocom/, unit =3D 1 NFiles =3D 98 SizExt =3D 524288 WInBl= k > =3D 512 > defal =3D T LstWrd =3D 233431552 FType=3D2 FMxFil=3D= 10000 > > Number 0 0 0 0 0 > 0 0 0 > Base 12203972 390144 495616 321536 12752384 > 10698752 201216 365568 > End 12204032 402432 527360 322048 12818944 > 11614208 201728 372736 > End1 12204032 402432 527360 322048 12818944 > 11614208 201728 372736 > Wr Pntr 12203972 388608 495616 321536 12533760 > 10698752 201216 365568 > Rd Pntr 12203972 388608 495616 321536 12533760 > 10698752 201216 365568 > Length 60 12288 31744 512 66560 > 915456 512 7168 > > (...) > > Error termination in NtrErr: > NtrErr Called from FileIO. > > > -------------------------------------------------------------------------= --------------------------------------------------------------------- > > Thanks in advance for any sugestion. > > Diego > UPV-ITQ > Spain. > > > > --=20 Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim^-^compchem.net Website: www.compchem.net Fax No.: +20862342601 --00163642652302bce30484ee5205 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear=A0Diego

I read your complain about= a=A0NtrErr =A0error. This type of errors happens in different cases, one of them= as Dave mentioned due to space issue, and in this case NMax information sh= ould be mentioned in last few lines, which is not available in the supporte= d information you gave. Another possibility is the checkpoint file, what ha= ppened is your checkpoint file has not be created, or optimization data (fo= r first cycle) has not be saved in your checkpoint file. that is what you h= ave got.

There= is no technical solve for this error. Just, try to build up your input fil= e again, save checkpoint file (%chk=3Dfilename.chk) and change its path.

If yo= u got the error again, you would send your input file and we can test it.

Since= rely;

M. Ib= rahim

On Thu, Apr 22, 2010 at 9:24 PM, DIEGOI= GOMEZ darkego21]_[yahoo.com <owner-chemistry^-^ccl.net= > wrote:

Hi Dave,
thanks for your reply!!

= I'm using Gaussian09 and my system is really small, I'm doing a tes= t with one Pd(II) atom in square planar stereo-chemistry with two H2O molec= ules and two OH- groups as ligands interacting with one H2 molecule.
---------------------------------------------------------------------------= -----------------------------------------
=A0=A0 118 basis functions,=A0= =A0 217 primitive gaussians,=A0=A0 124 cartesian basis functions
=A0=A0= =A0 29 alpha electrons=A0=A0=A0=A0=A0=A0 29 beta electrons
---------------------------------------------------------------------------= ----------------------------------------
Previously I did one MP2 optimi= zation of the system (without counterpoise) with no problems. So I don'= t believe that the Error is related with storage capacity (actually, I have done cal= culation on bigger systems with more than 300 basis functions). I speculate= that It seems to be related with the reading of some file or keyword when = the second step starts.

I forgot to mention that in this particular case the Pd cluster is fixe= d (opt=3Dz-matrix) an the optimization is only done on the H2 coordinates.<= br>
However I have not tried that option (%rwf), I'll give a look...=

Thanks again..

Diego
UPV-ITQ
Spain.
=20

From: "Close, David M. = CLOSED_._mail.etsu.edu" <owner-chemistry]~[ccl.net>
To: "Gomez, Diego Arman= do " <darkego21]~[ya= hoo.com>
Sent: Thu= , April 22, 2010 8:02:19 PM
Subject: CCL: Error terminat= ion in NtrErr at MP2 calculation.

=20 =20

From: owner-chemistry+closed=3D=3De= tsu.edu*ccl.net [mailto:owner= -chemistry+closed=3D=3Det= su.edu*ccl.net] On = Behalf Of DIEGOI GOMEZ darkego21 ~ yahoo.com<= /a>
Sent: Thursday, April 22, 2010 9:56 AM
To: Close, David M.
Subject: CCL: Error termination in NtrErr at MP2 calculation.=
=20

=A0
=20

Hello there.

I'm doing an optimization of a pair of interacting molecules at MP2 lev= el with simultaneous counterpoise correction. I'm using two basis set (lanl2dz = and 6-31G**) through the "GEN" keyword.=A0 The calculation starts without problems, so the first SCF cycle and the second-order perturbation = are accomplished. However, when the next step starts the follow Error is report= ed:

---------------------------------------------------------------------------= ------------------------------------------------------------------
=A0 ***** Axes restored to original set *****
=A0Cartesian Forces:=A0 Max=A0=A0=A0=A0 0.199455160 RMS=A0=A0=A0=A0 0.055013514
=A0Operation on file out of range.
FileIO: IOper=3D 2 IFilNo(1)=3D=A0 -522 Len=3D=A0=A0=A0=A0=A0=A0=A0=A0 118 IPos=3D=A0=A0=A0=A0=A0=A0=A0=A0 118 Q=3D=A0=A0 47965310131088

=A0dumping /fiocom/, unit =3D 1 NFiles =3D=A0=A0=A0 98 SizExt =3D=A0=A0=A0 524288 WInBlk =3D=A0=A0=A0=A0=A0=A0 512
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 defal =3D T LstWrd =3D=A0=A0 233431552 FType=3D2 FMxFil=3D10000

=A0Number=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0
=A0Base=A0=A0=A0=A0=A0 12203972=A0=A0=A0=A0 390144=A0=A0=A0=A0 495616=A0=A0=A0=A0 321536=A0=A0 12752384=A0=A0 10698752=A0=A0=A0=A0 201216=A0=A0=A0=A0 365568
=A0End=A0=A0=A0=A0=A0=A0 12204032=A0=A0=A0=A0 402432=A0=A0=A0=A0 527360=A0=A0=A0=A0 322048=A0=A0 12818944=A0=A0 11614208=A0=A0=A0=A0 201728=A0=A0=A0=A0 372736
=A0End1=A0=A0=A0=A0=A0 12204032=A0=A0=A0=A0 402432=A0=A0=A0=A0 527360=A0=A0=A0=A0 322048=A0=A0 12818944=A0=A0 11614208=A0=A0=A0=A0 201728=A0=A0=A0=A0 372736
=A0Wr Pntr=A0=A0 12203972=A0=A0=A0=A0 388608=A0=A0=A0=A0 495616=A0=A0=A0=A0 321536=A0=A0 12533760=A0=A0 10698752=A0=A0=A0=A0 201216=A0=A0=A0=A0 365568
=A0Rd Pntr=A0=A0 12203972=A0=A0=A0=A0 388608=A0=A0=A0=A0 495616=A0=A0=A0=A0 321536=A0=A0 12533760=A0=A0 10698752=A0=A0=A0=A0 201216=A0=A0=A0=A0 365568
=A0Length=A0=A0=A0=A0=A0=A0=A0=A0=A0 60=A0=A0=A0=A0=A0 12288=A0=A0=A0=A0=A0 31744=A0=A0=A0=A0=A0=A0=A0 512=A0=A0=A0=A0=A0 66560=A0=A0=A0=A0 915456=A0=A0=A0=A0=A0=A0=A0 512=A0=A0=A0=A0=A0=A0 7168

(...)
=20

=A0Error termination in NtrErr:
=A0NtrErr Called from FileIO.

---------------------------------------------------------------------------= -------------------------------------------------------------------

Thanks in advance for any sugestion.

Diego
UPV-ITQ
Spain.
=20

=A0
=20