Re: [gmx-users] is the D G sol of g_sas useless? why?
Felipe Villanelo wrote: Hi gmxs, I'm trying to compute a aproximated D G of binding between two proteins using a termodynamic cycle, and the D Gsol calculated with g_sas (from 10 ns dynamics for every situation) But I had read here, that the value this way calculated is useless why? First you have to check the literature. This calculation is based on a paper more than 20 years old, and the main feature of this calculation is it's simplicity. Second you have to verify that the calculation is done correctly... Waiting for answer - Felipe Villanelo Lizana Biochemist Laboratorio de Biología Estructural y Molecular Universidad de Chile ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: wierd behavior of mdrun
I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluster shows that the job is running, also the processors are 100% engaged while I have no outputs! A standard guess: what about trying to run the single-processor job on the same cluster? Does it run OK? -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, cell.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: gmx-users Digest, Vol 64, Issue 17
Dear Gerrit, On the website below you state all basissets were available. I tried to use 6-311G* and got an error message stating 6-311G* wasn't available. Have you implemented in the meantime? Or is there any extra installation package required? I use gromacs-4.0.5 My question about Frequency calculation was aiming at the necessity of calculating the Zero-Point energy. I thought I needed it for getting the right energies, since Single Point Calculations only consider the absolute minimum, don't they? Best wishes, Ilona Quoting Gerrit Groenhof ggro...@gwdg.de: THere is documentation available in the manual and at wwwuser.gwdg.de/~ggroenh/qmmm.html If you need a SP computation, do a zero-step MD run: nsteps=0 Frequencies can only be computed numerically I think, but I never tried this. Best, Gerrit 7. QMMM settings (ilona.bal...@bioquant.uni-heidelberg.de) Dear Gerrit, I am using Gromacs/Gaussian for qmmm-calculations. From the manual I could only find the instructions for how to use qmmm the normal way, i.e. fill in the mdp file, but I learned from other Gromacs users that adding additional keywords was possible. How? Where do I put them? Is there any documentation available on what the standard settings are? i.e. every default qm step is a single-point calculation, right? Is a zero point calculation included yet? If not, how can I change from SP to frequency calculation? Best wishes and thanks in advance, Ilona -- ___ 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/search before posting! End of gmx-users Digest, Vol 64, Issue 17 * ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Ilona Baldus MPI Stuttgart INF 276 69120 Heidelberg Tel.: 06221-5451268 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] table extension
Thanks Mark. I am simulating a dimer in vacuum, and it is my understanding that once a non-bonded interaction has exceeded the table-extension cutoff this interaction will NOT be included in the potential for the remaining simulation, even if it will later come back to a distance within the table-extension. Your answer helped me. It is now a matter of choosing the box dimensions table extension that will be reasonable yet not increase the computation time too much. --Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Wed, Aug 26, 2009 at 16:03, Mark Abraham mark.abra...@anu.edu.au wrote: Probably not... if you're asking this question because you suspect something's not working properly, you might get enlightenment/a fix quicker if you're more explicit :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] table extension
Hi, No, this is not correct. A interaction beyond the cut-off + table-extension will get a random energy and force depending on what is stored in the memory of your computer beyond the table___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] optimization of gromacs 4.0.5 on AIX Power6
Dear All Has anybody tried version 4.0.5 on an IBM Power6 (4.7Ghz) cluster? We have installed the program with the following configure options (using fftw we installed separately): ./configure --with-fft=fftw2 --enable-mpi --enable-float CC=mpcc_r F77=mpxlf_r CXX=mpCC_r CFLAGS=-O3 -qarch=pwr6 -qtune=pwr6 -qcpluscmt It compiles and works but the performance is poor compared to our Opteron Cluster (2.6Ghz) For example with 8 procs for a small protein in water we get 5.8ns/+day compared to 9.6 ns/day on the Linux cluster, which is a bit disappointing. Since there alot of compiler options to play with we would be grateful if somebody who has already found a good set would share them with us. best wishes Silvia Giuliani ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] grompp.mdp
Hi, I am going to analyse the normal mode analysis of n-butane. For this I donloaded a PDB id .Then opened in wordpad and just took the glu residue.Opend it on viewerpro and deleted the -COO, NH2,-CH2 portion to make it n-butane.Then made a pdb file and ran in GROMACS. I suceesfully created the topology file and did the next steps .But grompp showed the following error abhi...@scfbioserver project]$ grompp -v -f em.mdp -c ab.gro -p ab.top -o ab.tp r :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.0.4 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c ab.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p ab.top InputTopology file -pp processed.top Output, Opt. Topology file -o ab.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 380 of the 1326 non-bonded parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file ab.top, line 126]: System has non-zero total charge: -1.00e-00 processing coordinates... --- Program grompp, VERSION 4.0.4 Source code file: grompp.c, line: 362 Fatal error: number of coordinates in coordinate file (ab.gro, 13) does not match topology (ab.top, 29602) --- A Lady Shaves Her Legs (C. Meijering) So my questioin is my way of procedding is wrong or right? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] PULL CODE AND NpT ensemble
Hi all, I would like to use pull code to evaluate the free energy of pulling system1 from system2. Free energy calculation should be done for NpT ensemble. All tutorials found for calculating free energy used 1) berensen for T and P coupling or 2) berensen for T coupling AND Parrinelo for P coupling or 3)Vrescale for T and no P coupling I am a bit lost in which one should lead to real ensemble. Is any one could help? Regards, geraldine, phD? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] grompp.mdp
Hi kayal, Well, given that it reads Fatal error your final question seems a bit odd, doesn't it? How did you obtain the topology? Apparently, there's a bit more specified in it than a single butane! Besides, I notice that you use the GROMOS force field, which is a united atom force field. That means that aliphatic hydrogens are collapsed onto the bearing C atoms. Ergo, butane in a UA force field will count exactly four atoms. But you have thirteen in your coordinate file. Maybe it would be a good idea to read up a bit on the background of MD: force fields, topologies, etc. Most tutorials, although commonly aimed at proteins, will introduce these concepts and give you a feel for the matter. Tsjerk On Thu, Aug 27, 2009 at 1:20 PM, abhijit kayalkayalabhijiti...@gmail.com wrote: Hi, I am going to analyse the normal mode analysis of n-butane. For this I donloaded a PDB id .Then opened in wordpad and just took the glu residue.Opend it on viewerpro and deleted the -COO, NH2,-CH2 portion to make it n-butane.Then made a pdb file and ran in GROMACS. I suceesfully created the topology file and did the next steps .But grompp showed the following error abhi...@scfbioserver project]$ grompp -v -f em.mdp -c ab.gro -p ab.top -o ab.tp r :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.0.4 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c ab.gro Input Structure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p ab.top Input Topology file -pp processed.top Output, Opt. Topology file -o ab.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 380 of the 1326 non-bonded parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file ab.top, line 126]: System has non-zero total charge: -1.00e-00 processing coordinates... --- Program grompp, VERSION 4.0.4 Source code file: grompp.c, line: 362 Fatal error: number of coordinates in coordinate file (ab.gro, 13) does not match topology (ab.top, 29602) --- A Lady Shaves Her Legs (C. Meijering) So my questioin is my way of procedding is wrong or right?
RE: [gmx-users] PULL CODE AND NpT ensemble
Hi, I would use v-rescale and Berendsen pressure coupling. Although Berendsen pressure coupling, strictly speaking, does not give the correct ensemble, in practice it produces negligible artifacts, unless you are looking at pressure/volume fluctuations. Berk To: gmx-users@gromacs.org Date: Thu, 27 Aug 2009 07:20:00 -0400 From: gigita...@aol.fr Subject: [gmx-users] PULL CODE AND NpT ensemble Hi all, I would like to use pull code to evaluate the free energy of pulling system1 from system2. Free energy calculation should be done for NpT ensemble. All tutorials found for calculating free energy used 1) berensen for T and P coupling or 2) berensen for T coupling AND Parrinelo for P coupling or 3)Vrescale for T and no P coupling I am a bit lost in which one should lead to real ensemble. Is any one could help? Regards, geraldine, phD _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re : [gmx-users] PULL CODE AND NpT ensemble
Hi Berk, Thanks for your answer. I just want to be sure that the procedure is correct. No I do not look at the pressure/volume fluctutation. But I do want to make a clever choice of the ensemble so that no significant extra artifact are generated, since the number of contraint to be calculated is not negligible. I previously used no P coupling and I was wondering is that feature could explain that the average force plot is not smooth function. Other criteria such as Cut-off value for LJ and coulomb may also be checked out? Geraldine -E-mail d'origine- De : Berk Hess g...@hotmail.com A : Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Jeudi, 27 Août 2009 13:45 Sujet : RE: [gmx-users] PULL CODE AND NpT ensemble Hi, I would use v-rescale and Berendsen pressure coupling. Although Berendsen pressure coupling, strictly speaking, does not give the correct ensemble, in practice it produces negligible artifacts, unless you are looking at pressure/volume fluctuations. Berk To: gmx-users@gromacs.org Date: Thu, 27 Aug 2009 07:20:00 -0400 From: gigita...@aol.fr Subject: [gmx-users] PULL CODE AND NpT ensemble Hi all, I would like to use pull code to evaluate the free energy of pulling system1 from system2. Free energy calculation should be done for NpT ensemble. All tutorials found for calculating free energy used 1) berensen for T and P coupling or 2) berensen for T coupling AND Parrinelo for P coupling or 3)Vrescale for T and no P coupling I am a bit lost in which one should lead to real ensemble. Is any one could help? Regards, geraldine, phD Express yourself instantly with MSN Messenger! MSN Messenger= ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] optimization of gromacs 4.0.5 on AIX Power6
Silvia Giuliani wrote: Dear All Has anybody tried version 4.0.5 on an IBM Power6 (4.7Ghz) cluster? We have installed the program with the following configure options (using fftw we installed separately): ./configure --with-fft=fftw2 --enable-mpi --enable-float CC=mpcc_r F77=mpxlf_r CXX=mpCC_r CFLAGS=-O3 -qarch=pwr6 -qtune=pwr6 -qcpluscmt It compiles and works but the performance is poor compared to our Opteron Cluster (2.6Ghz) For example with 8 procs for a small protein in water we get 5.8ns/+day compared to 9.6 ns/day on the Linux cluster, which is a bit disappointing. Since there alot of compiler options to play with we would be grateful if somebody who has already found a good set would share them with us. If this processor does not support PowerPC Altivec, then the reason is straightforward. GROMACS gets its speed from optimized non-bonded interaction kernels, and your machine doesn't have any written for it. You can see in the .log file whether generic or optimized kernels are being used. Optimized kernels exist for x86s, so they're fast. Given the above assumptions, your GROMACS installation will be using generic kernels written in C. You should certainly try the --enable-fortran configure flag to see if the equivalent in FORTRAN is better optimized by the compiler. You can try -O4 or -O5, but these tend to have little utility for GROMACS. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] table extension
Thanks. And what happens if later on it comes back to the cut-off + table-extension range? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 11:13, Berk Hess g...@hotmail.com wrote: A interaction beyond the cut-off + table-extension will get a random energy and force depending on what is stored in the memory of your computer beyond the table ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] optimization of gromacs 4.0.5 on AIX Power6
I believe that this problem is about mpi installation. What mpi version was installed ? Lampi or openmpi. There is a good tutorial about that in http://www.gromacs.org/WIKI-import/Quick_and_Dirty_Installation Best regards, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Thu, Aug 27, 2009 at 7:14 AM, Silvia Giuliani silvia.giuli...@cineca.itwrote: Dear All Has anybody tried version 4.0.5 on an IBM Power6 (4.7Ghz) cluster? We have installed the program with the following configure options (using fftw we installed separately): ./configure --with-fft=fftw2 --enable-mpi --enable-float CC=mpcc_r F77=mpxlf_r CXX=mpCC_r CFLAGS=-O3 -qarch=pwr6 -qtune=pwr6 -qcpluscmt It compiles and works but the performance is poor compared to our Opteron Cluster (2.6Ghz) For example with 8 procs for a small protein in water we get 5.8ns/+day compared to 9.6 ns/day on the Linux cluster, which is a bit disappointing. Since there alot of compiler options to play with we would be grateful if somebody who has already found a good set would share them with us. best wishes Silvia Giuliani ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Pressure for froozen atoms
Hi guys, does gromacs use the following scheme to calculate the virial/pressure for systems including froozen atoms: http://www.ccp5.ac.uk/infoweb/wsmith22/wsmith22/wsmith22.html ?? Thx, Alex ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Pressure for froozen atoms
Hi, Gromacs does not do anything special for frozen atoms. You have to make sure that you do not calculate forces between frozen atoms, if you want the virial to be correct. Berk Date: Thu, 27 Aug 2009 14:46:47 +0200 From: alexander.h...@mytum.de To: gmx-users@gromacs.org Subject: [gmx-users] Pressure for froozen atoms Hi guys, does gromacs use the following scheme to calculate the virial/pressure for systems including froozen atoms: http://www.ccp5.ac.uk/infoweb/wsmith22/wsmith22/wsmith22.html ?? Thx, Alex ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] table extension
Omer Markovitch wrote: Thanks. And what happens if later on it comes back to the cut-off + table-extension range? It would look up a non-random energy and force. If the code never noticed the distance was out-of-range, it won't notice it come back into range either. Mark Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 11:13, Berk Hess g...@hotmail.com wrote: A interaction beyond the cut-off + table-extension will get a random energy and force depending on what is stored in the memory of your computer beyond the table ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: Re : [gmx-users] PULL CODE AND NpT ensemble
Hi, There are no settings that matter in particular for pulling compared to a normal simulation. All the settings that matter normally matter here as well. NVT pulling should give nearly identical results no NPT, as long as you set the volume correctly. Berk To: gmx-users@gromacs.org Subject: Re : [gmx-users] PULL CODE AND NpT ensemble Date: Thu, 27 Aug 2009 08:03:56 -0400 From: gigita...@aol.fr Hi Berk, Thanks for your answer. I just want to be sure that the procedure is correct. No I do not look at the pressure/volume fluctutation. But I do want to make a clever choice of the ensemble so that no significant extra artifact are generated, since the number of contraint to be calculated is not negligible. I previously used no P coupling and I was wondering is that feature could explain that the average force plot is not smooth function. Other criteria such as Cut-off value for LJ and coulomb may also be checked out? Geraldine -E-mail d'origine- De : Berk Hess g...@hotmail.com A : Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Jeudi, 27 Août 2009 13:45 Sujet : RE: [gmx-users] PULL CODE AND NpT ensemble Hi, I would use v-rescale and Berendsen pressure coupling. Although Berendsen pressure coupling, strictly speaking, does not give the correct ensemble, in practice it produces negligible artifacts, unless you are looking at pressure/volume fluctuations. Berk To: gmx-users@gromacs.org Date: Thu, 27 Aug 2009 07:20:00 -040 0 From: gigita...@aol.fr Subject: [gmx-users] PULL CODE AND NpT ensemble Hi all, I would like to use pull code to evaluate the free energy of pulling system1 from system2. Free energy calculation should be done for NpT ensemble. All tutorials found for calculating free energy used 1) berensen for T and P coupling or 2) berensen for T coupling AND Parrinelo for P coupling or 3)Vrescale for T and no P coupling I am a bit lost in which one should lead to real ensemble. Is any one could help? Regards, geraldine, phD Express yourself instantly with MSN Messenger! MSN Messenger= ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www in terface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Pressure for froozen atoms
Hi together, You have to make sure that you do not calculate forces between frozen atoms, is it enough to include in grompp.mdp such command: ; Non-equilibrium MD stuff freezegrps = S freezedim= Y Y Y ;Energy group exclusion for position restraints energygrps = A S energygrp_excl = S S Or it excludes only energy calculations, but not forces? Regards, Leonid From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Berk Hess [g...@hotmail.com] Sent: Thursday, August 27, 2009 2:59 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] Pressure for froozen atoms Hi, Gromacs does not do anything special for frozen atoms. You have to make sure that you do not calculate forces between frozen atoms, if you want the virial to be correct. Berk Date: Thu, 27 Aug 2009 14:46:47 +0200 From: alexander.h...@mytum.de To: gmx-users@gromacs.org Subject: [gmx-users] Pressure for froozen atoms Hi guys, does gromacs use the following scheme to calculate the virial/pressure for systems including froozen atoms: http://www.ccp5.ac.uk/infoweb/wsmith22/wsmith22/wsmith22.html ?? Thx, Alex ___ 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/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/mailing_lists/users.php See all the ways you can stay connected to friends and familyhttp://www.microsoft.com/windows/windowslive/default.aspx ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] table extension
But what if the gmx code did notice it? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 16:21, Mark Abraham mark.abra...@anu.edu.au wrote: It would look up a non-random energy and force. If the code never noticed the distance was out-of-range, it won't notice it come back into range either. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] table extension
There is a misunderstanding here about noticing. For efficiency reasons, the code does not check if atoms are beyond the table length. So the code does not care about or notice anything. However, you do care, since you do not want random forces. (Although in nearly all cases the force will be, or zero: fine, no artifacts, or 10^30: immediate crash of mdrun). Berk Date: Thu, 27 Aug 2009 17:18:13 +0300 Subject: Re: [gmx-users] table extension From: omer...@gmail.com To: gmx-users@gromacs.org But what if the gmx code did notice it? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 16:21, Mark Abraham mark.abra...@anu.edu.au wrote: It would look up a non-random energy and force. If the code never noticed the distance was out-of-range, it won't notice it come back into range either. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: Re: [gmx-users] is the D G sol of g_sas useless? why?
Is true, the paper is old, but is an simply aproximation Besides that, do you know other simply way for protein-protein DG bind from dynamics (but not g_lie) ? Thanks anyway - Felipe Villanelo Lizana Biochemist Laboratorio de Biología Estructural y Molecular Universidad de Chile ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Pressure for froozen atoms
That's enough for the non-bonded interactions. Energy group exclusions work on both the energy and the forces. But if you have bonded interactions between atoms in S you also need to exclude those. Note that this only matters if you want to have the pressure. Berk From: yel...@uni-mainz.de To: gmx-users@gromacs.org Date: Thu, 27 Aug 2009 16:13:42 +0200 Subject: RE: [gmx-users] Pressure for froozen atoms Hi together, You have to make sure that you do not calculate forces between frozen atoms, is it enough to include in grompp.mdp such command: ; Non-equilibrium MD stuff freezegrps = S freezedim= Y Y Y ;Energy group exclusion for position restraints energygrps = A S energygrp_excl = S S Or it excludes only energy calculations, but not forces? Regards, Leonid From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Berk Hess [g...@hotmail.com] Sent: Thursday, August 27, 2009 2:59 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] Pressure for froozen atoms Hi, Gromacs does not do anything special for frozen atoms. You have to make sure that you do not calculate forces between frozen atoms, if you want the virial to be correct. Berk Date: Thu, 27 Aug 2009 14:46:47 +0200 From: alexander.h...@mytum.de To: gmx-users@gromacs.org Subject: [gmx-users] Pressure for froozen atoms Hi guys, does gromacs use the following scheme to calculate the virial/pressure for systems including froozen atoms: http://www.ccp5.ac.uk/infoweb/wsmith22/wsmith22/wsmith22.html ?? Thx, Alex ___ 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/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/mailing_lists/users.php See all the ways you can stay connected to friends and familyhttp://www.microsoft.com/windows/windowslive/default.aspx ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_energy and g_analyze give different averages
When analysing FEP simulations. After running g_energy -f fep000.edr -f2 fep_000-005.edr for obtaining the dF = -kT ln exp(-(EB-EA)/kT) A I tried to obtain the standard deviation for this ensemble average using g_analyze -f runavg.xvg, but I've noticed that the average values are quite different___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] g_energy and g_analyze give different averages
Ragnarok sdf wrote: When analysing FEP simulations. After running g_energy -f fep000.edr -f2 fep_000-005.edr for obtaining the dF = -kT ln exp(-(EB-EA)/kT) A I tried to obtain the standard deviation for this ensemble average using g_analyze -f runavg.xvg, but I've noticed that the average values are quite different g_energy takes all values during your simulation into account, g_analyze only the printed datapoints. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] wierd behavior of mdrun
One more point: when I run the job interactively, although it works but date and time are wrong! step 0 step 100, will finish Wed Sep 16 16:16:00 2009 step 200, will finish Wed Sep 16 14:32:34 2009 step 300, will finish Wed Sep 16 13:57:51 2009 step 400, will finish Wed Sep 16 11:35:46 2009 step 500, will finish Wed Sep 16 11:50:12 2009 step 600, will finish Wed Sep 16 10:36:38 2009 step 700, will finish Wed Sep 16 09:44:04 2009 step 800, will finish Wed Sep 16 10:07:02 2009 step 900, will finish Wed Sep 16 09:29:25 2009 step 1000, will finish Wed Sep 16 08:59:19 2009 step 1100, will finish Wed Sep 16 09:20:06 2009 step 1200, will finish Wed Sep 16 08:55:47 2009 step 1300, will finish Wed Sep 16 09:13:38 2009 step 1400, will finish Wed Sep 16 08:53:15 2009 Is it a cluster related or GROMACS related issue? Is it important at all? Payman On Wed, 2009-08-26 at 22:06 -0600, Paymon Pirzadeh wrote: I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluster shows that the job is running, also the processors are 100% engaged while I have no outputs! Here is my mdp file: title= Yo cpp = cpp include = -I../top define = -DPOSRES ; Run control integrator = md dt = 0.001 ;1 fs nsteps = 300 ;3 ns comm_mode= linear nstcomm = 1 ;Output control nstxout = 5000 nstlog = 5000 nstenergy= 5000 nstxtcout= 1500 nstvout = 5000 nstfout = 5000 xtc_grps = energygrps = ; Neighbour Searching nstlist = 10 ns_type = grid rlist= 0.9 pbc = xyz ; Electrostatistics coulombtype = PME rcoulomb = 0.9 ;epsilon_r= 1 ; Vdw vdwtype = cut-off rvdw = 1.2 DispCorr = EnerPres ;Ewald fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 optimize_fft= yes ; Temperature coupling tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t= 0.1 ref_t= 275 ; Pressure Coupling Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 5.5e-5 ;ref_p= 1.0 gen_vel = yes gen_temp = 275 gen_seed = 173529 constraint-algorithm = Lincs constraints = all-bonds lincs-order = 4 I am not sure where things go wrong! Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: g_energy and g_analyze give different averages
Is there a correct way to obtain the standard deviation for these data sets? Ragnarok sdf wrote: When analysing FEP simulations. After running g_energy -f fep000.edr -f2 fep_000-005.edr for obtaining the dF = -kT ln exp(-(EB-EA)/kT) A I tried to obtain the standard deviation for this ensemble average using g_analyze -f runavg.xvg, but I've noticed that the average values are quite different g_energy takes all values during your simulation into account, g_analyze only the printed datapoints. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Using make_ndx
Hi everyone, I'm trying to figure out the right commands for make_ndx so to generate the correct index.ndx file for g_bond analysis. From my PDB file: ATOM 1 BN0 GGA X 1 107.255 17.133 66.368 1.00 0.00 P1 C ATOM 2 SC1 GGA X 1 110.304 14.942 66.116 1.00 0.00 P1 C ATOM 3 SC2 GGA X 1 113.632 15.318 65.904 1.00 0.00 P1 C ATOM 4 SC3 GGA X 1 114.063 12.624 65.310 1.00 0.00 P1 C ATOM 5 BN0 GGA X 2 108.171 20.156 68.028 1.00 0.00 P1 C ATOM 6 SC1 GGA X 2 109.535 18.753 71.242 1.00 0.00 P1 C ATOM 7 SC2 GGA X 2 112.445 17.547 72.396 1.00 0.00 P1 C ATOM 8 SC3 GGA X 2 111.301 16.592 74.758 1.00 0.00 P1 C ATOM 9 BN0 GGA X 3 110.843 21.726 66.258 1.00 0.00 P1 C ATOM 10 SC1 GGA X 3 111.984 24.201 68.852 1.00 0.00 P1 C ATOM 11 SC2 GGA X 3 114.049 24.264 71.496 1.00 0.00 P1 C ATOM 12 SC3 GGA X 3 113.142 26.763 72.351 1.00 0.00 P1 C ..rest of PDB file not included... Say I want to group together atoms SC1, SC2, and SC3 from all GGA residues in make_ndx: 0 System : 19699 atoms 1 GGA : 472 atoms 2 DRG : 324 atoms 3 W : 18669 atoms 4 ION : 234 atoms I typed in: r GGA t SC1 | r GGA t SC2 | r GGA t SC3 Found 472 atoms with residue name GGA Found 36 atoms with type SC1 Merged two groups with AND: 472 36 - 0 Found 472 atoms with residue name GGA Merged two groups with OR: 0 472 - 472 Found 24 atoms with type SC2 Merged two groups with AND: 472 24 - 0 Found 472 atoms with residue name GGA Merged two groups with OR: 0 472 - 472 Found 0 atoms with type SC3 5 GGA__SC1_GGA__SC2_GGA: 472 atoms However, make_ndx found 0 atoms with type SC3. I'm not sure if I'm doing this correctly. If anyone has any insight, I would be most appreciative. Thanks, L ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Using make_ndx
Lili Peng wrote: Hi everyone, I'm trying to figure out the right commands for make_ndx so to generate the correct index.ndx file for g_bond analysis. From my PDB file: ATOM 1 BN0 GGA X 1 107.255 17.133 66.368 1.00 0.00 P1 C ATOM 2 SC1 GGA X 1 110.304 14.942 66.116 1.00 0.00 P1 C ATOM 3 SC2 GGA X 1 113.632 15.318 65.904 1.00 0.00 P1 C ATOM 4 SC3 GGA X 1 114.063 12.624 65.310 1.00 0.00 P1 C ATOM 5 BN0 GGA X 2 108.171 20.156 68.028 1.00 0.00 P1 C ATOM 6 SC1 GGA X 2 109.535 18.753 71.242 1.00 0.00 P1 C ATOM 7 SC2 GGA X 2 112.445 17.547 72.396 1.00 0.00 P1 C ATOM 8 SC3 GGA X 2 111.301 16.592 74.758 1.00 0.00 P1 C ATOM 9 BN0 GGA X 3 110.843 21.726 66.258 1.00 0.00 P1 C ATOM 10 SC1 GGA X 3 111.984 24.201 68.852 1.00 0.00 P1 C ATOM 11 SC2 GGA X 3 114.049 24.264 71.496 1.00 0.00 P1 C ATOM 12 SC3 GGA X 3 113.142 26.763 72.351 1.00 0.00 P1 C ...rest of PDB file not included... Say I want to group together atoms SC1, SC2, and SC3 from all GGA residues in make_ndx: 0 System : 19699 atoms 1 GGA : 472 atoms 2 DRG : 324 atoms 3 W : 18669 atoms 4 ION : 234 atoms I typed in: r GGA t SC1 | r GGA t SC2 | r GGA t SC3 Found 472 atoms with residue name GGA Found 36 atoms with type SC1 Merged two groups with AND: 472 36 - 0 Found 472 atoms with residue name GGA Merged two groups with OR: 0 472 - 472 Found 24 atoms with type SC2 Merged two groups with AND: 472 24 - 0 Found 472 atoms with residue name GGA Merged two groups with OR: 0 472 - 472 Found 0 atoms with type SC3 5 GGA__SC1_GGA__SC2_GGA: 472 atoms However, make_ndx found 0 atoms with type SC3. I'm not sure if I'm doing this correctly. You're not, or else it would have worked :) Better approach: r GGA a SC1 SC2 SC3 In order to specify atom *types* you must be using a run input file (.tpr), and SC1, SC2, and SC3 are atom *names* in the .pdb file, but not necessarily their type. -Justin If anyone has any insight, I would be most appreciative. Thanks, L ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
[gmx-users] Re: wierd behavior of mdrun
Then I believe you have problems with MPI. Before I experienced something alike on our old system - serial version worked OK but parallel one failed. The same issue was with CPMD by the way. Another programs worked fine. I didn't correct that problem... On Thu, Aug 27, 2009 at 7:14 PM, Paymon Pirzadehppirz...@ucalgary.ca wrote: Yes, it works when it is run on one processor interactively! On Thu, 2009-08-27 at 09:23 +0300, Vitaly V. Chaban wrote: I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluster shows that the job is running, also the processors are 100% engaged while I have no outputs! A standard guess: what about trying to run the single-processor job on the same cluster? Does it run OK? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] error in ATOM2CG.awk script
Dear all, I was earlier facing problem regarding the mismatch of atoms in .top and .gro file and then after useful discussion here I figured out that some atoms were missing in my cg.pdb file and that problem is because of the OLDER atom2cg.awk script which MARTINI folks have in their website. When I was using the earlier version of atom2cg.awk script I had 776 atoms in my .gro file and 804 atoms in .itp file and thats why .top and .gro were not matching but again the same problem raised even after using the new atom2cg.awk script which they sent me but it included some ILE residues and now I have 784 atoms in .gro file and 804 atoms in .itp file I pretty much now know how to fix the script but I am confused in some of the things like: 1) In the cleaned.pdb file of my protein the ARG residue in the atom2cg.awk script takes only CA, CG and NE with BN0, SC1, and SC2. If I want to include other atoms as well like NH1, NH2, CZ, CD etc what should I print for these atoms (either BN0, SC1, or SC2). As a matter of fact I don't know what do SC1, BN0, SC2 mean? So, i don't know while adding other atoms for ARG residue what should I print for them and I searched in the martini website but could not find anything. Please let me know if you got my problem. Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] LINCS
tekle...@ualberta.ca wrote: Hi Justin, There is something physically unrealistic about your model You are right! The main problem I found out is that some of the structures in my Solution broke down.. I used ... genbox -cp .grob -nmol 20 -ci insert.gro -cs spc216.gro XXX.top -XX.gro To generate multiple structures in a box. However, it creates overlap and my orginal structures broke down. I checked the structures! Using -ci and -cs simultaneously typically breaks down. Use -ci to add your molecules, then in a separate step, use -cs to solvate the box. -Justin Can you please let me how to generate multiple structures in a fixed box at random or packed in a solutio (e.g water) Thank you for you help Robella Quoting Justin A. Lemkul jalem...@vt.edu: tekle...@ualberta.ca wrote: Hi Justin, I tried to run full MD after energy minimization in both vacuo and water... went good but I got this ERROR once I try to run full MD. Can you please help. There is something physically unrealistic about your model. That's the case whenever you see a LINCS warning. Without a more complete description of what you've done (minimization and equilibration protocol, initial construction of the model, etc) and the details of your simulation parameters, there's nothing more anyone can really say beyond a guess. It appears that the wiki is down at the moment, but these pages have useful information (when the site comes back up): http://oldwiki.gromacs.org/index.php/blowing_up http://oldwiki.gromacs.org/index.php/Errors And since LINCS errors have been posted thousands of times to the list, the archive should have some useful advice as well, so search here: http://oldwww.gromacs.org/swish-e/search/search2.php -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
Re: [gmx-users] error in ATOM2CG.awk script
sunny mishra wrote: Dear all, I was earlier facing problem regarding the mismatch of atoms in .top and .gro file and then after useful discussion here I figured out that some atoms were missing in my cg.pdb file and that problem is because of the OLDER atom2cg.awk script which MARTINI folks have in their website. When I was using the earlier version of atom2cg.awk script I had 776 atoms in my .gro file and 804 atoms in .itp file and thats why .top and .gro were not matching but again the same problem raised even after using the new atom2cg.awk script which they sent me but it included some ILE residues and now I have 784 atoms in .gro file and 804 atoms in .itp file As I recall, the root problem was that the original .pdb file from the RCSB had missing atoms that you had not properly modeled back in. I pretty much now know how to fix the script but I am confused in some of the things like: 1) In the cleaned.pdb file of my protein the ARG residue in the atom2cg.awk script takes only CA, CG and NE with BN0, SC1, and SC2. If I want to include other atoms as well like NH1, NH2, CZ, CD etc what should I print for these atoms (either BN0, SC1, or SC2). As a matter of fact I don't know what do SC1, BN0, SC2 mean? Hence the point of CG. You don't account for every single atom that was in the atomistic structure. BN0 = backbone particle, SC1 and SC2 are side chain particles that will be given specific attributes in the topology. You should probably refer to the MARTINI publications for a more clear understanding of how the force field was conceived and how it should be used. -Justin So, i don't know while adding other atoms for ARG residue what should I print for them and I searched in the martini website but could not find anything. Please let me know if you got my problem. Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
Re: [gmx-users] optimization of gromacs 4.0.5 on AIX Power6
Rodrigo faccioli wrote: I believe that this problem is about mpi installation. What mpi version was installed ? Lampi or openmpi. That would be plausible on a home-built linux cluster, but not so likely on a cluster bought from a recognized vendor like IBM, whose MPI installation should be dependable. Mark There is a good tutorial about that in http://www.gromacs.org/WIKI-import/Quick_and_Dirty_Installation Best regards, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Thu, Aug 27, 2009 at 7:14 AM, Silvia Giuliani silvia.giuli...@cineca.itwrote: Dear All Has anybody tried version 4.0.5 on an IBM Power6 (4.7Ghz) cluster? We have installed the program with the following configure options (using fftw we installed separately): ./configure --with-fft=fftw2 --enable-mpi --enable-float CC=mpcc_r F77=mpxlf_r CXX=mpCC_r CFLAGS=-O3 -qarch=pwr6 -qtune=pwr6 -qcpluscmt It compiles and works but the performance is poor compared to our Opteron Cluster (2.6Ghz) For example with 8 procs for a small protein in water we get 5.8ns/+day compared to 9.6 ns/day on the Linux cluster, which is a bit disappointing. Since there alot of compiler options to play with we would be grateful if somebody who has already found a good set would share them with us. best wishes Silvia Giuliani ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
