[gmx-users] Re: efficient use of pme with gromacs
Hi Léo, please keep Gromacs-related issues on the Gromacs-users mailing list. This will give others with similar problems the possibility to profit from already answered questions by searching this list. Also, please choose a descriptive subject (I have done that for you). Thank you! The message you see DD step 543999 vol min/aver 0.331 load imb.: force 76.6% pme mesh/force 0.909 is just meant for your information, meaning that the PME mesh processors finish their calculation earlier than the short-range Coulomb force processors. To balance that optimally, please use the g_tune_pme tool that is provided since version 4.5. If you need this tool for 4.0, look here: http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ The DD info message is however no reason for mdrun to stop. So there must be another problem here. Can you find an error message in any of the output files? Best, Carsten On Sep 21, 2010, at 8:01 PM, Léo Degrève wrote: Prof. Kutzner, I found papers and other materials that you have published on the efficient use of pme with the gromacs software. I have a problem that maybe you can help me, if you wish, to solve since I didn’t found what to do. Using gromacs on 96 processors the program stops systematically after warnings like: DD step 543999 vol min/aver 0.331 load imb.: force 76.6% pme mesh/force 0.909 Defining –npme according to grompp, the result is the same. Is there a solution? Thank you for your attention. Léo Degrève Grupo de Simulação Molecular Departamento de Química - FFCLRP Universidade de São Paulo Av. Bandeirantes, 3900 14040-901 Ribeirão Preto - SP Brazil Fax: +55 (16) 36024838 Fone: +55 (16) 3602-3688/ 3602-4372 e-mail: l...@obelix.ffclrp.usp.br l...@ffclrp.usp.br http://obelix.ffclrp.usp.br Sent via the WebMail system at srv1.ffclrp.usp.br -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Natalie Stephenson wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Are you making manual updates, or allowing genbox/genion to make changes for you? In the case of the former, check your work :) In the case of the latter, I'd be more concerned. There really is nothing diagnostic that can be done. You simply have to check how many of each molecule are in your system. Something has gone wrong somewhere along the way. http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Thanks for your help Justin Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Terry [terrence...@gmail.com] Sent: 22 September 2010 11:55 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.ukmailto:natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Ok ... think I've worked out what's happened ... There were two 'SOL' groups. So when replacing solvent with ions it has added double the amount of ions to the topol.top file. Think I'll go back a couple of steps and try to sort out why there are two 'SOL' groups. Thanks for the help! xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] Sent: 22 September 2010 13:02 To: Discussion list for GROMACS users Subject: RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Thanks for your help Justin Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Terry [terrence...@gmail.com] Sent: 22 September 2010 11:55 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.ukmailto:natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Natalie Stephenson wrote: Ok ... think I've worked out what's happened ... There were two 'SOL' groups. So when replacing solvent with ions it has added double the amount of ions to the topol.top file. Think I'll go back a couple of steps and try to sort out why there are two 'SOL' groups. Were there water molecules (i.e., from a crystal structure) in the initial structure passed to pdb2gmx? -Justin Thanks for the help! xxx *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] *Sent:* 22 September 2010 13:02 *To:* Discussion list for GROMACS users *Subject:* RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Thanks for your help Justin Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Terry [terrence...@gmail.com] *Sent:* 22 September 2010 11:55 *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.uk mailto:natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Yeah ... hadn't realised they were there when I began the simulating Natalie xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 22 September 2010 13:37 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Natalie Stephenson wrote: Ok ... think I've worked out what's happened ... There were two 'SOL' groups. So when replacing solvent with ions it has added double the amount of ions to the topol.top file. Think I'll go back a couple of steps and try to sort out why there are two 'SOL' groups. Were there water molecules (i.e., from a crystal structure) in the initial structure passed to pdb2gmx? -Justin Thanks for the help! xxx *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] *Sent:* 22 September 2010 13:02 *To:* Discussion list for GROMACS users *Subject:* RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Thanks for your help Justin Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Terry [terrence...@gmail.com] *Sent:* 22 September 2010 11:55 *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.uk mailto:natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REg QM/MM Mdrun error
Very very thank you sir; further when i run Mdrun after energy minimisatins by following command ./mdrun_d -s spep_em.tpr -o spep_em.trr -c spep_b4pr.gro -g em.log I got errror as follows i am using Mopac/gromacs intrface QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 14 QMlevel: MP2/STO-3G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 Segmentation fault (core dumped) what could i do to rectify this error i am expecting your gem of reply --- On Tue, 21/9/10, Gerrit Groenhof ggro...@gwdg.de wrote: From: Gerrit Groenhof ggro...@gwdg.de Subject: [gmx-users] QM/MM topology fiels problem To: gmx-users@gromacs.org Date: Tuesday, 21 September, 2010, 4:16 PM Please read the error message: it says that you need no parameters for your conn bonds. Gerrit Message: 2 Date: Tue, 21 Sep 2010 14:58:40 +0530 (IST) From: vidhya sankarscvsankar_...@yahoo.com Subject: [gmx-users] QM/MM topology fiels problem To: gmx-users@gromacs.org Message-ID:277598.19746...@web95503.mail.in.yahoo.com Content-Type: text/plain; charset=utf-8 Dear gromacs users , thank you for your reply when i run the ./grompp it shows the error as follows ./grompp_d -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 222 of the 1653 non-bonded parameter combinations --- Program grompp_d, VERSION 4.0.7 Source code file: toppush.c, line: 1379 Fatal error: Incorrect number of parameters - found 2, expected 0 or 0 for Connect Bonds what could i do to avod error? i am expecting your valuable reply -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100921/ece4e258/attachment-0001.html -- Message: 3 Date: Tue, 21 Sep 2010 11:57:22 +0200 (MEST) From: Fabio Affinitof.affin...@cineca.it Subject: Re: [gmx-users] error on compilation on BlueGene/P To: Discussion list for GROMACS usersgmx-users@gromacs.org Message-ID:4c988143.9020...@cineca.it Content-Type: text/plain; charset=ISO-8859-1 Like for the frontend, the --enable-fortran is the problem. Maybe it could be useful to update the instruction page :) Fabio On 09/21/2010 10:54 AM, Mark Abraham wrote: - Original Message - From: Fabio Affinitof.affin...@cineca.it Date: Tuesday, September 21, 2010 18:51 Subject: Re: [gmx-users] error on compilation on BlueGene/P To: Discussion list for GROMACS usersgmx-users@gromacs.org Thank you, Mark and Berk! your suggestion was helpful and I successfully compiled on the frontend.Now I have a problem when I compile on the compute nodes. Configure was fine with these parameters: ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --host=ppc --build=ppc64 --enable-ppc-sqrt=1 \ --disable-ppc-altivec \ --enable-bluegene --enable-fortran --enable-mpi \ --with-fft=fftw3 \ --program-suffix=_mpi_bg \ --without-x \ CC=mpixlc_r \ CFLAGS=-O3 -qarch=450d -qtune=450 \ MPICC=mpixlc_r CXX=mpixlC_r \ CXXFLAGS=-O3 -qarch=450d -qtune=450 \ CPPFLAGS=-I/bgp/userinternal/cin0644a/fftwlibs/include \ F77=mpixlf77_r FFLAGS=-O3 -qarch=auto -qtune=auto \ LDFLAGS=-L/bgp/userinternal/cin0644a/fftwlibs/lib \ LIBS=-lmass But when I compile using make mdrun the compilation stops in this way. creating libgmxpreprocess_mpi.la (cd .libs rm -f libgmxpreprocess_mpi.la ln -s ../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la) make[1]: *** No rule to make target `../mdlib/libmd_mpi.la', needed by `mdrun'. Stop. make[1]: Leaving directory `/bgp/userinternal/cin0644a/gmx/bgp/src/kernel' Any suggestion? Thanks! Normally that would be symptomatic of an earlier error in make (or maybe configure). Please check carefully. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] Re: gmx-users Digest, Vol 77, Issue 142
Why do you try to do MP2. Mopac will only allow semi-empirical methods. Though that does not seem to be the source of the error. Gerrit further when i run Mdrun after energy minimisatins by following command ./mdrun_d -s spep_em.tpr -o spep_em.trr -c spep_b4pr.gro -g em.log I got errror as follows i am using Mopac/gromacs intrface QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 14 QMlevel: MP2/STO-3G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 Segmentation fault (core dumped) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] reg QM/MM mdrun error
THAHNKS for your reply when i trying with AM1/STO-3Gi got error as follows Program mdrun_d, VERSION 4.0.7 Source code file: qmmm.c, line: 684 Fatal error: Semi-empirical QM only supported with Mopac is there is any installation problem in Mopac/gromacs?. i have succesfully installed No compilation error during installation? THEN WHAT WILL BE THE SOURCE OF ERROR I expecting your worthfull reply --- On Wed, 22/9/10, Gerrit Groenhof ggro...@gwdg.de wrote: From: Gerrit Groenhof ggro...@gwdg.de Subject: [gmx-users] Re: gmx-users Digest, Vol 77, Issue 142 To: gmx-users@gromacs.org Date: Wednesday, 22 September, 2010, 7:10 PM Why do you try to do MP2. Mopac will only allow semi-empirical methods. Though that does not seem to be the source of the error. Gerrit further when i run Mdrun after energy minimisatins by following command ./mdrun_d -s spep_em.tpr -o spep_em.trr -c spep_b4pr.gro -g em.log I got errror as follows i am using Mopac/gromacs intrface QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 14 QMlevel: MP2/STO-3G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 Segmentation fault (core dumped) -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] reg QM/MM mdrun error
Did you try to run a pure QM job using MOPAC as well as running a pure MD job using GROMACS? This might be a good start before trying to mix the two On 09/22/2010 04:25 PM, vidhya sankar wrote: THAHNKS for your reply when i trying with AM1/STO-3Gi got error as follows Program mdrun_d, VERSION 4.0.7 Source code file: qmmm.c, line: 684 Fatal error: Semi-empirical QM only supported with Mopac is there is any installation problem in Mopac/gromacs?. i have succesfully installed No compilation error during installation? THEN WHAT WILL BE THE SOURCE OF ERROR I expecting your worthfull reply -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb2gmx eats a bond
Hi all, i have built an .rtp entry for a molecule with 310 bonds, for the opls force field. For pdb2gmx i use the following command (version 4.0.7) *pdb2gmx -f CAT.pdb -o -p -ignh -ter* -ter is there because it is no protein, and use no C- and N-terminus (since there are none). Her one question, the option -ter works (i think) but it is not listed with pdb2gmx -h Are there any reasons. The relevant output line of pdb2gmx is then *Number of bonds was 310, now 309* - So pdb2gmx ate a bond. Has anybody an idea why this happens? Has anybody an idea which could be the fastest way to find out which bond is missing? Are the [ angles ] and [ dihedrals ] section also affected by this (since if i understood it correctly pdb2gmx uses the [ bonds ] section to determine the other two sections)? Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx eats a bond
Thomas Schlesier wrote: Hi all, i have built an .rtp entry for a molecule with 310 bonds, for the opls force field. For pdb2gmx i use the following command (version 4.0.7) *pdb2gmx -f CAT.pdb -o -p -ignh -ter* -ter is there because it is no protein, and use no C- and N-terminus (since there are none). Her one question, the option -ter works (i think) but it is not listed with pdb2gmx -h Are there any reasons. The -ter option is listed for me in 4.0.7: /usr/local/gmx_407/bin/pdb2gmx -h ... -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged ... The option certainly works, if that's the concern. The relevant output line of pdb2gmx is then *Number of bonds was 310, now 309* - So pdb2gmx ate a bond. Has anybody an idea why this happens? I don't know all of the underlying code, but I frequently see a bond removed from most of my protein structures. Has anybody an idea which could be the fastest way to find out which bond is missing? Run a short MD and see if any of your atoms drift away :) Are the [ angles ] and [ dihedrals ] section also affected by this (since if i understood it correctly pdb2gmx uses the [ bonds ] section to determine the other two sections)? Potentially, but until you test to see if any bonds are actually missing, there's nothing to diagnose in these sections. -Justin Greetings Thomas -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Issue with Atom Types/Charges/Mass when including ATP in gromos53.a6
Dear all, I want to run some simulations of a kinase with an ATP molecule using gromacs 4.5.1 with the gromos53a6.ff forcefield. To generate the .gro and .top files I am running pdb2gmx -v -f ATP.pdb -p initial.top -o initial.gro -ff gromos53a6 -water spc Now the generated topology file shows some odd atom types, charges, and masses which differ from the ones found in the ATP-entry of gromos53a6.ff: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NR476ATPAN9 1 -0.214.0067 ; qtot -0.2 2 O476ATPAC4 2 0 1.48594e-41 ; qtot -0.2 I played a bit with the chain-termini etc. but could not fix the issue and guess I must be doing some silly mistake. I would therefore greatly appreciate some help/pointers. Thank you, Alex ps: ## ATP.pdb (just the ATP-molecule, when I take the entire complex of protein structure+ATP I get the same issues) ATOM 3826 APB ATP D 476 47.748 48.397 59.538 0.00227.61 ATOM 3827 AO3B ATP D 476 47.540 49.729 58.745 0.00227.61 ATOM 3828 AO2B ATP D 476 49.145 48.068 60.002 0.00227.61 ATOM 3829 AO1B ATP D 476 47.038 47.146 58.965 0.00227.61 ATOM 3830 APA ATP D 476 46.063 49.828 61.632 0.00227.61 ATOM 3831 AO1A ATP D 476 44.574 49.457 61.408 0.00227.61 ATOM 3832 AO2A ATP D 476 46.341 51.157 61.156 0.00227.61 ATOM 3833 AO3A ATP D 476 46.956 48.594 60.969 0.00227.61 ATOM 3834 AO5* ATP D 476 46.560 49.512 63.160 0.00227.61 ATOM 3835 AC5* ATP D 476 48.092 49.215 63.245 0.00227.61 ATOM 3836 AC4* ATP D 476 48.454 48.749 64.571 0.00227.61 ATOM 3837 AO4* ATP D 476 47.347 48.436 65.439 0.00227.61 ATOM 3838 AC3* ATP D 476 49.180 47.483 64.374 0.00227.61 ATOM 3839 AO3* ATP D 476 50.540 47.515 64.449 0.00227.61 ATOM 3840 AC2* ATP D 476 48.751 46.656 65.478 0.00227.61 ATOM 3841 AO2* ATP D 476 49.542 46.012 66.564 0.00227.61 ATOM 3842 AC1* ATP D 476 47.572 47.225 66.121 0.00227.61 ATOM 3843 AN9 ATP D 476 46.374 46.469 65.860 0.00227.61 ATOM 3844 AC8 ATP D 476 45.367 46.820 65.035 0.00227.61 ATOM 3845 AN7 ATP D 476 44.404 45.853 64.941 0.00227.61 ATOM 3846 AC5 ATP D 476 44.697 44.807 65.844 0.00227.61 ATOM 3847 AC6 ATP D 476 44.103 43.545 66.341 0.00227.61 ATOM 3848 AN6 ATP D 476 42.813 43.067 65.910 0.00227.61 ATOM 3849 AN1 ATP D 476 45.064 42.708 67.074 0.00227.61 ATOM 3850 AC2 ATP D 476 46.255 43.142 67.280 0.00227.61 ATOM 3851 AN3 ATP D 476 46.786 44.335 66.975 0.00227.61 ATOM 3852 AC4 ATP D 476 46.065 45.198 66.246 0.00227.61 ATOM 3853 APG ATP D 476 47.198 49.717 57.298 0.00227.61 ATOM 3854 AO1G ATP D 476 47.583 50.876 56.391 0.00227.61 ATOM 3855 AO2G ATP D 476 47.441 48.310 56.911 0.00227.61 ATOM 3856 AO3G ATP D 476 45.690 49.283 57.490 0.00227.61 # from initial.top [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 476 ATP rtp ATP q +0.7 1 NR476ATPAN9 1 -0.214.0067 ; qtot -0.2 2 O476ATPAC4 2 0 1.48594e-41 ; qtot -0.2 3 NR476ATPAN3 3 -0.3614.0067 ; qtot -0.56 4 O476ATPAC2 4 0 1.48594e-41 ; qtot -0.56 5 O476ATPAN1 5 0 1.48594e-41 ; qtot -0.56 6 C476ATPAC6 6 0.36 12.011 ; qtot -0.2 7 NT476ATPAN6 7 -0.8314.0067 ; qtot -1.03 8 H476ATP AH61 7 0.415 1.008 ; qtot -0.615 9 H476ATP AH62 7 0.415 1.008 ; qtot -0.2 10 O476ATPAC5 8 0 1.48594e-41 ; qtot -0.2 11 NR476ATPAN7 9 -0.3614.0067 ; qtot -0.56 12 O476ATPAC8 10 0 1.48594e-41 ; qtot -0.56 13 O476ATP AC1* 11 0 1.48594e-41 ; qtot -0.56 14 OA476ATP AO4* 12 -0.3615.9994 ; qtot -0.92 15CH1476ATP AC4* 12 0.16 13.019 ; qtot -0.76 16 O476ATP AC2* 13 0 1.48594e-41 ; qtot -0.76 17 OA476ATP AO2* 14 -0.54815.9994 ; qtot -1.308 18 H476ATP AH2* 14 0.398 1.008 ; qtot -0.91 19 O476ATP AC3* 15 0 1.48594e-41 ; qtot -0.91 20 OA476ATP AO3* 16 -0.54815.9994 ; qtot -1.458 21 H476ATP AH3* 16 0.398
Re: [gmx-users] Tables with forcefield
On 21/09/10 20:45, Sai Pooja wrote: I wanted to change the interactions between the Protein and Solvent so I tried using tables with the potential function scaled by a constant value. I wanted to use this in combination with forcefield parameters (charmm). I changed the combination rule in the forcefield.itp file from '2' to '1' since tables use C6 and C12 values. To test the system I started with default tables. When I run grompp, it generates the .tpr file successfully but in the md simulation using mdrun, settle does not converge. It does not converge for 1 water molecule. If I go back to the combination rule '2' in the forcefield.itp file, I get a warning that using combination rule 2 with tables may generate error. With combination rule '2' and cutoff for both vanderwaals and coulombtype, i face no problem. I use combination rule 1; but I also define all tabulated interactions for all possible *pairs* under the [ nonbond_params ] section, so the combination rule actually doesn't matter much. Does this mean that one cannot use tables with forcefield parameters? I am not sure of understanding with question -can you clarify? Massimo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: pdb2gmx eats a bond
You are right, overlooked the line. And thanks for the idea with the short run, i'm happy with anything, so that i don't must look into more then 300 bonds. Greetings Thomas Thomas Schlesier wrote: Hi all, i have built an .rtp entry for a molecule with 310 bonds, for the opls force field. For pdb2gmx i use the following command (version 4.0.7) *pdb2gmx -f CAT.pdb -o -p -ignh -ter* -ter is there because it is no protein, and use no C- and N-terminus (since there are none). Her one question, the option -ter works (i think) but it is not listed with pdb2gmx -h Are there any reasons. The -ter option is listed for me in 4.0.7: /usr/local/gmx_407/bin/pdb2gmx -h ... -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged ... The option certainly works, if that's the concern. The relevant output line of pdb2gmx is then *Number of bonds was 310, now 309* - So pdb2gmx ate a bond. Has anybody an idea why this happens? I don't know all of the underlying code, but I frequently see a bond removed from most of my protein structures. Has anybody an idea which could be the fastest way to find out which bond is missing? Run a short MD and see if any of your atoms drift away :) Are the [ angles ] and [ dihedrals ] section also affected by this (since if i understood it correctly pdb2gmx uses the [ bonds ] section to determine the other two sections)? Potentially, but until you test to see if any bonds are actually missing, there's nothing to diagnose in these sections. -Justin Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Question about building and testing on imac
Hello, I built gromacs4.5.1 on my new imac (OS X 10.6.4) without problems using the command sequence: ./configure --enable-shared make make install Before that, I built fftw (3.2.2) by following the following sequence: ./configure --enable-threads --enable-float make make install However, most of the tests (./gmxtest.pl simple and ./gmxtest.pl complex) FAILED. Could this be explained by the fact I'm using gcc4.2? If so, how can I compile with gcc4.0? If not, what could be the problem? I've tried this a couple of times (using single and double precisions) and got the same FAILED messages in all cases. Thanks in advance, Silvia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question about building and testing on imac
Silvia Crivelli wrote: Hello, I built gromacs4.5.1 on my new imac (OS X 10.6.4) without problems using the command sequence: ./configure --enable-shared make make install Before that, I built fftw (3.2.2) by following the following sequence: ./configure --enable-threads --enable-float make make install However, most of the tests (./gmxtest.pl simple and ./gmxtest.pl complex) FAILED. Could this be explained by the fact I'm using gcc4.2? If so, how can I compile with gcc4.0? If not, what could be the problem? I've tried this a couple of times (using single and double precisions) and got the same FAILED messages in all cases. The test suite is not very robust, so some failures are expected. The mechanism for using pdb2gmx has changed somewhat, and in the absence of updates to the test set, many of those test probably fail because the commands simply aren't being run correctly. -Justin Thanks in advance, Silvia -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] atomtype problem (was Re: gmx-users Digest, Vol 77, Issue 138)
I've gone ahead and changed the subject line to potentially attract the attention of others who might help. lloyd riggs wrote: Dear All, I'm not sure if this is a bug or not. I downloaded and installed the new version of Gromacs, and compiled it fine, and recompiled just mdrun_mpi The problem I now encounter. U was using 53a6 FF, which worked in the past, although I am partial to all atoms. In Pro residues, the topolog output from grompp lables three of the CH2 in the ring as CH2r. When I then do an EM or MD, gromacs complains that it can not find atom type CH2r. I looked through all the .itp, .rtp and amino acid definitions, and CH2r is there. If I re-lable the topology and .gro file by hand to CHR1 the system works, but the overall geometry is slightly off (if you look at the atom definitions and take into account that prolines are not completly aeromatic, only partially... Well, proline isn't aromatic at all, but CHR1 will try to force the atoms to be planar. None of this should be necessary (nor is it right to do). In any case, is this a bug or is there some other problem I missed? I did look at the input .pdb file, and the same nomenclature I used before with the same ff now does not work? All signs point to the fact that processing of proline should work out of the box, so to speak. The CH2r atom type is properly defined in all the relevant files. Can you post a bit more detail, like the exact error message, snippet from the topology, etc? I haven't had any problem with proline-containing proteins with 53a6 in the newest version. -Justin Sincerely Stephan Watkins -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Issue with Atom Types/Charges/Mass when including ATP in gromos53.a6
Hi, I am not sure why there is not an error message but something is going very wrong (from looking at the topology produced by pdb2gmx). I have had issues (in older versions of GROMACS) where the four letter naming of atoms for ATP in GROMOS has caused problems. I tried your pdb with the letter 'A' removed from before all of the atom names and with the corresponding entries the aminoacids.rtp and aminoacids.hdb files also updated. With this I get the correct topology. Again I am not sure why you don't get an error from pdb2gmx, maybe someone else can comment on this or maybe you should file a bugzilla. Cheers Tom On 22/09/10 17:49, asc...@ctbp.ucsd.edu wrote: Dear all, I want to run some simulations of a kinase with an ATP molecule using gromacs 4.5.1 with the gromos53a6.ff forcefield. To generate the .gro and .top files I am running pdb2gmx -v -f ATP.pdb -p initial.top -o initial.gro -ff gromos53a6 -water spc Now the generated topology file shows some odd atom types, charges, and masses which differ from the ones found in the ATP-entry of gromos53a6.ff: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NR476ATPAN9 1 -0.214.0067 ; qtot -0.2 2 O476ATPAC4 2 0 1.48594e-41 ; qtot -0.2 I played a bit with the chain-termini etc. but could not fix the issue and guess I must be doing some silly mistake. I would therefore greatly appreciate some help/pointers. Thank you, Alex ps: ## ATP.pdb (just the ATP-molecule, when I take the entire complex of protein structure+ATP I get the same issues) ATOM 3826 APB ATP D 476 47.748 48.397 59.538 0.00227.61 ATOM 3827 AO3B ATP D 476 47.540 49.729 58.745 0.00227.61 ATOM 3828 AO2B ATP D 476 49.145 48.068 60.002 0.00227.61 ATOM 3829 AO1B ATP D 476 47.038 47.146 58.965 0.00227.61 ATOM 3830 APA ATP D 476 46.063 49.828 61.632 0.00227.61 ATOM 3831 AO1A ATP D 476 44.574 49.457 61.408 0.00227.61 ATOM 3832 AO2A ATP D 476 46.341 51.157 61.156 0.00227.61 ATOM 3833 AO3A ATP D 476 46.956 48.594 60.969 0.00227.61 ATOM 3834 AO5* ATP D 476 46.560 49.512 63.160 0.00227.61 ATOM 3835 AC5* ATP D 476 48.092 49.215 63.245 0.00227.61 ATOM 3836 AC4* ATP D 476 48.454 48.749 64.571 0.00227.61 ATOM 3837 AO4* ATP D 476 47.347 48.436 65.439 0.00227.61 ATOM 3838 AC3* ATP D 476 49.180 47.483 64.374 0.00227.61 ATOM 3839 AO3* ATP D 476 50.540 47.515 64.449 0.00227.61 ATOM 3840 AC2* ATP D 476 48.751 46.656 65.478 0.00227.61 ATOM 3841 AO2* ATP D 476 49.542 46.012 66.564 0.00227.61 ATOM 3842 AC1* ATP D 476 47.572 47.225 66.121 0.00227.61 ATOM 3843 AN9 ATP D 476 46.374 46.469 65.860 0.00227.61 ATOM 3844 AC8 ATP D 476 45.367 46.820 65.035 0.00227.61 ATOM 3845 AN7 ATP D 476 44.404 45.853 64.941 0.00227.61 ATOM 3846 AC5 ATP D 476 44.697 44.807 65.844 0.00227.61 ATOM 3847 AC6 ATP D 476 44.103 43.545 66.341 0.00227.61 ATOM 3848 AN6 ATP D 476 42.813 43.067 65.910 0.00227.61 ATOM 3849 AN1 ATP D 476 45.064 42.708 67.074 0.00227.61 ATOM 3850 AC2 ATP D 476 46.255 43.142 67.280 0.00227.61 ATOM 3851 AN3 ATP D 476 46.786 44.335 66.975 0.00227.61 ATOM 3852 AC4 ATP D 476 46.065 45.198 66.246 0.00227.61 ATOM 3853 APG ATP D 476 47.198 49.717 57.298 0.00227.61 ATOM 3854 AO1G ATP D 476 47.583 50.876 56.391 0.00227.61 ATOM 3855 AO2G ATP D 476 47.441 48.310 56.911 0.00227.61 ATOM 3856 AO3G ATP D 476 45.690 49.283 57.490 0.00227.61 # from initial.top [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 476 ATP rtp ATP q +0.7 1 NR476ATPAN9 1 -0.214.0067 ; qtot -0.2 2 O476ATPAC4 2 0 1.48594e-41 ; qtot -0.2 3 NR476ATPAN3 3 -0.3614.0067 ; qtot -0.56 4 O476ATPAC2 4 0 1.48594e-41 ; qtot -0.56 5 O476ATPAN1 5 0 1.48594e-41 ; qtot -0.56 6 C476ATPAC6 6 0.36 12.011 ; qtot -0.2 7 NT476ATPAN6 7 -0.8314.0067 ; qtot -1.03 8 H476ATP AH61 7 0.415 1.008 ; qtot -0.615 9 H476ATP AH62 7 0.415 1.008 ; qtot -0.2 10 O476ATPAC5 8 0 1.48594e-41 ; qtot -0.2 11 NR476ATPAN7 9 -0.3614.0067 ; qtot -0.56 12 O476ATPAC8 10 0 1.48594e-41 ; qtot -0.56 13 O476
[gmx-users] rlist and rlistlong and grompp notes in gmx451
Dear Gromacs Users and Developers, I am testing gromacs-4.5.1 with different running parameters, in particular switching potentials and rlistlong, I have a question about this NOTEs: NOTE 1 [file qua.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb. NOTE 2 [file qua.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. I am using: rlist= 1.2 rlistlong= 1.5 coulombtype = pme-switch rcoulomb-switch = 1.0 rcoulomb = 1.2 vdw-type = switch rvdw-switch = 1.0 rvdw = 1.2 with rlist=rvdw=rcoulomb because I thought that was rlonglist that should be longer than rvdw and rcoulomb. If rlist should be larger than rvdw what's the use of rlonglist? Thanks, Carlo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: rotational correlation function
Dear Dr. Chaban, I meant the N-H bond vectors of protein backbone for calculation of rotational time correlation function to calculate the rotational diffusion constant of my protein. I need a protocol which walks me step by step through the procedure. Thanks for your Attention. Paymon On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote: Message: 2 Date: Wed, 22 Sep 2010 12:07:27 -0600 From: Paymon Pirzadeh ppirz...@ucalgary.ca Subject: [gmx-users] rotational correlation function To: gmx-users@gromacs.org Message-ID: 1285178847.11669.66.ca...@paymon-desktop Content-Type: text/plain Hello, Imagine if the total correlation function of a protein could be factorized into rotational and internal portions: Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t) and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)? What does the g_rms -fit do? I am confused on how I can use gromacs commands on my output files. Sorry for mass of e-mails. Paymon Hey, Paymon - Do you mean the correlation function of the velocity (VACF)? Why not to use g_velacc and g_rotacf for translational and rotational VACFs? I suppose, your molecule is rigid (enough) for rotational velocoty to make sense. -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14627-0216 United States of America -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: rotational correlation function
Hmm... Rotational time..? If you need diffusion constant, just use g_rotacf and then integrate the resulting VACF. If I recall correctly, you should make an index file with three numbers to define two vectors for the calculation. On Wed, Sep 22, 2010 at 7:27 PM, Paymon Pirzadeh ppirz...@ucalgary.ca wrote: Dear Dr. Chaban, I meant the N-H bond vectors of protein backbone for calculation of rotational time correlation function to calculate the rotational diffusion constant of my protein. I need a protocol which walks me step by step through the procedure. Thanks for your Attention. Paymon On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote: Message: 2 Date: Wed, 22 Sep 2010 12:07:27 -0600 From: Paymon Pirzadeh ppirz...@ucalgary.ca Subject: [gmx-users] rotational correlation function To: gmx-users@gromacs.org Message-ID: 1285178847.11669.66.ca...@paymon-desktop Content-Type: text/plain Hello, Imagine if the total correlation function of a protein could be factorized into rotational and internal portions: Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t) and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)? What does the g_rms -fit do? I am confused on how I can use gromacs commands on my output files. Sorry for mass of e-mails. Paymon Hey, Paymon - Do you mean the correlation function of the velocity (VACF)? Why not to use g_velacc and g_rotacf for translational and rotational VACFs? I suppose, your molecule is rigid (enough) for rotational velocoty to make sense. -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14627-0216 United States of America -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: rotational correlation function
On Wed, Sep 22, 2010 at 7:47 PM, Paymon Pirzadeh ppirz...@ucalgary.ca wrote: Well, I found a paper: J. Chem Phys. Vol. 131, 155103 (2009) in which they have used GROMACS and its utilities to calculate the correlation functions I need, however, it is not clear to me what utilities were used and what steps were taken. Since They are using the N-H vector, it is only two points. I believe the third point is another N or H site of the same protein. Vitaly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
