[gmx-users] Shared library version binary on CYGWIN
Dear Mark and GROMACS users: Mark wrote. You can't build DLLs since the cygwin build tools are unix-style, and the GROMACS build strategy is unix-specific. --enable-shared also probably won't work for unix-style shared libraries, because the dynamic linker is probably the Windows ld.exe, which can't deal with unix-style shared libraries. Thanks a lot for the comment. It would be possible to make GROMACS write proper DLLs using the cygwin dlltool functionality, but nobody has ever cared enough to do it. I'd struggle to imagine a useful Windows environment where providing 100MB of statically-linked executables was a serious problem. I found the libtool within gromacs source (both 3.3.3 and 4.0.4) is not as new as that of e.g. fftw-3.2.1 (which use the libtool-2.2.6). I'm wondering if the libtool version was updated to the newer one, then the DLLs could be generated properly, because fftw-3.2.1 can build DLL on cygwin if it configured with --enable-shared. I'd tried that with gromacs a little but no success as I have no detailed knowledge on GNU autotools. For a course, you won't even need the whole executable set. mdrun, grompp, editconf, pdb2gmx, genion, g_energy, trjconv and maybe one or two more analysis tools to suit the course should do it. You're right. That may be a practical solution in the current situation. Kind Regards. Makoto Yoneya, Dr. AIST, Japan ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Lennard-Jones 9-6 potential problems
Firstly, thanks Berk and David van der Spoel for your replies. Maybe I have not explain my problems clearly, there is only one type of particle,namely one full-atom benzene molecule is replaced by one coarse-grained benzene particle,so there in no non-bonded interactions between different types and comb-rule may not work. in the [ defaults ] section of the ITP file, the defaults power for the repulsion term is 12, if I change it to 9, is that enough if I want to use LJ-9-6 potential? is there still anything needed to be changed? Best regards! Hi, I forgot about this feature. Your problem is indeed that you used comb-rule=1, you have to use 2 or 3 to make this work. And indeed you should use user tables filled with the 9-6 potential. Gromacs could actually easily support p-6 tables with any value for p, by storing p in the tpr file and automatically using tables when p!=12. Berk Date: Tue, 26 May 2009 09:45:22 +0200 From: sp...@xray.bmc.uu.se To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Lennard-Jones 9-6 potential problems zhangjianguo2002 wrote: Hi everyone! Have anyone used the Lennard-Jones 9-6 potential for coarse-grained models? when I use it, I get a very different result from that is got from the same Lennard-Jones 9-6 potential formed a potential table,the latter's results are comparable to the experiments. when I use LJ-9-6 potential,the ITP file is as following: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 9 Even if this may generate the correct parameters (please use gmxdump to check your tpr file) you still have to provide a user table to mdrun and to set vdw-type = user in your mdp file. You may need to change the nbfunc to three as well. Check source code in src/kernel/convparm to see what is going on. I don't think this is documented anywhere, is it? [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon opls_001 Cx 6 78.01900A0.5052.95; [ moleculetype ] ; Name nrexcl Phenyl 1 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_001 1 Phenyl C1 10.000 78.0190 other files ,such as mdp file and top file ,are all the same as normal LJ-12-6 potential, are these correct if I want to use LJ-9-6 potential? Do I still need to change something? Thanks very much for your kindness! ´©Ô½µØÕð´ø ¼ÍÄîãë´¨µØÕðÒ»ÖÜÄê http://512.mail.163.com/mailstamp/stamp/dz/activity.do?from=footer ___ gmx-users mailing listgmx-us...@gromacs.org http://www.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.sespoel@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-us...@gromacs.org http://www.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 -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090526/2143fc5e/attachment.html -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 61, Issue 124 ** 穿越地震带 纪念汶川地震一周年 穿越地震带 纪念汶川地震一周年___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Lennard-Jones 9-6 potential problems
zhangjianguo2002 wrote: Firstly, thanks Berk and David van der Spoel for your replies. Maybe I have not explain my problems clearly, there is only one type of particle,namely one full-atom benzene molecule is replaced by one coarse-grained benzene particle,so there in no non-bonded interactions between different types and comb-rule may not work. in the [ defaults ] section of the ITP file, the defaults power for the repulsion term is 12, if I change it to 9, is that enough if I want to use LJ-9-6 potential? is there still anything needed to be changed? That is not enough. Please read carefully our previous answers. Best regards! Hi, I forgot about this feature. Your problem is indeed that you used comb-rule=1, you have to use 2 or 3 to make this work. And indeed you should use user tables filled with the 9-6 potential. Gromacs could actually easily support p-6 tables with any value for p, by storing p in the tpr file and automatically using tables when p!=12. Berk Date: Tue, 26 May 2009 09:45:22 +0200 From: sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] Lennard-Jones 9-6 potential problems zhangjianguo2002 wrote: Hi everyone! Have anyone used the Lennard-Jones 9-6 potential for coarse-grained models? when I use it, I get a very different result from that is got from the same Lennard-Jones 9-6 potential formed a potential table,the latter's results are comparable to the experiments. when I use LJ-9-6 potential,the ITP file is as following: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 9 Even if this may generate the correct parameters (please use gmxdump to check your tpr file) you still have to provide a user table to mdrun and to set vdw-type = user in your mdp file. You may need to change the nbfunc to three as well. Check source code in src/kernel/convparm to see what is going on. I don't think this is documented anywhere, is it? [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon opls_001 Cx 6 78.01900A0.5052.95; [ moleculetype ] ; Name nrexcl Phenyl 1 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_001 1 Phenyl C1 10.000 78.0190 other files ,such as mdp file and top file ,are all the same as normal LJ-12-6 potential, are these correct if I want to use LJ-9-6 potential? Do I still need to change something? Thanks very much for your kindness! ´©Ô½µØÕð´ø ¼ÍÄîãë´¨µØÕðÒ»ÖÜÄê http://512.mail.163.com/mailstamp/stamp/dz/activity.do?from=footer ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.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 mailto: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.se mailto:sp...@xray.bmc.uu.se sp...@gromacs.org mailto:sp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.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 mailto: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 -- next part -- An HTML attachment was scrubbed... URL:
Re: [gmx-users] Lennard-Jones 9-6 potential problems
zhangjianguo2002 wrote: Firstly, thanks Berk and David van der Spoel for your replies. Maybe I have not explain my problems clearly, there is only one type of particle,namely one full-atom benzene molecule is replaced by one coarse-grained benzene particle,so there in no non-bonded interactions between different types and comb-rule may not work. in the [ defaults ] section of the ITP file, the defaults power for the repulsion term is 12, if I change it to 9, is that enough if I want to use LJ-9-6 potential? is there still anything needed to be changed? The text on manual page 112 says this works, but table 5.3 on page 106 doesn't mention it. One or the other needs updating. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Lennard-Jones 9-6 potential problems
zhangjianguo2002 wrote: Firstly, thanks Berk and David van der Spoel for your replies. Maybe I have not explain my problems clearly, there is only one type of particle,namely one full-atom benzene molecule is replaced by one coarse-grained benzene particle,so there in no non-bonded interactions between different types and comb-rule may not work. in the [ defaults ] section of the ITP file, the defaults power for the repulsion term is 12, if I change it to 9, is that enough if I want to use LJ-9-6 potential? is there still anything needed to be changed? That is not enough. Please read carefully our previous answers. Thanks very much for your suggestions! I just want to use LJ-9-6 potential by providing sigma and epsilon parameters, that would be easer to change the potential by changing sigma and epsilon values than by changing potential table, does GROMACS support this ? or does GROMACS only support potential tables if the power of the repulsion term is not 12 ? Best regards! Hi, I forgot about this feature. Your problem is indeed that you used comb-rule=1, you have to use 2 or 3 to make this work. And indeed you should use user tables filled with the 9-6 potential. Gromacs could actually easily support p-6 tables with any value for p, by storing p in the tpr file and automatically using tables when p!=12. Thanks for your reply, do you mean that if p !=12 ,I have to change p to the value I want ,at the same time I have to provide a potential table according to LJ-P-6? Berk Date: Tue, 26 May 2009 09:45:22 +0200 From: sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] Lennard-Jones 9-6 potential problems zhangjianguo2002 wrote: Hi everyone! Have anyone used the Lennard-Jones 9-6 potential for coarse-grained models? when I use it, I get a very different result from that is got from the same Lennard-Jones 9-6 potential formed a potential table,the latter's results are comparable to the experiments. when I use LJ-9-6 potential,the ITP file is as following: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 9 Even if this may generate the correct parameters (please use gmxdump to check your tpr file) you still have to provide a user table to mdrun and to set vdw-type = user in your mdp file. You may need to change the nbfunc to three as well. Check source code in src/kernel/convparm to see what is going on. I don't think this is documented anywhere, is it? Thanks very much for your advice! According to you , I provide a user table( Does this mean that LJ'parameters epsilon and sigma setted in the ITP file don't work ? ) and set vdw-type = user as well as change nbfunc to three ,but grompp reports some errors that : Invalid nonbond function selector '3' using LJ,I read the manual again,it says : non-bond type =1(Lennaed-Jones) or 2(Buckingham), that is seemed that 3 is a illegal choice, is there something wrong? [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon opls_001 Cx 6 78.01900A0.505 2.95; [ moleculetype ] ; Name nrexcl Phenyl 1 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_001 1 Phenyl C1 10.000 78.0190 other files ,such as mdp file and top file ,are all the same as normal LJ-12-6 potential, are these correct if I want to use LJ-9-6 potential? Do I still need to change something? Thanks very much for your kindness! ´©Ã½µÃÃð´ø ¼ÃÃîãë´¨µÃÃðûÃÃÃê http://512.mail.163.com/mailstamp/stamp/dz/activity.do?from=footer ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.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 mailto: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.
Re: [gmx-users] Lennard-Jones 9-6 potential problems
zhangjianguo2002 wrote: zhangjianguo2002 wrote: Firstly, thanks Berk and David van der Spoel for your replies. Maybe I have not explain my problems clearly, there is only one type of particle,namely one full-atom benzene molecule is replaced by one coarse-grained benzene particle,so there in no non-bonded interactions between different types and comb-rule may not work. in the [ defaults ] section of the ITP file, the defaults power for the repulsion term is 12, if I change it to 9, is that enough if I want to use LJ-9-6 potential? is there still anything needed to be changed? That is not enough. Please read carefully our previous answers. Thanks very much for your suggestions! I just want to use LJ-9-6 potential by providing sigma and epsilon parameters, that would be easer to change the potential by changing sigma and epsilon values than by changing potential table, does GROMACS support this ? or does GROMACS only support potential tables if the power of the repulsion term is not 12 ? It is the other way around. GROAMCS only support native code for 12-6 and Exp-6, for everything else you need tables. But grompp can compute the C9,C6 params from eps/sig. Use gmxdump to check your input. Best regards! Hi, I forgot about this feature. Your problem is indeed that you used comb-rule=1, you have to use 2 or 3 to make this work. And indeed you should use user tables filled with the 9-6 potential. Gromacs could actually easily support p-6 tables with any value for p, by storing p in the tpr file and automatically using tables when p!=12. Thanks for your reply, do you mean that if p !=12 ,I have to change p to the value I want ,at the same time I have to provide a potential table according to LJ-P-6? Berk Date: Tue, 26 May 2009 09:45:22 +0200 From: sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] Lennard-Jones 9-6 potential problems zhangjianguo2002 wrote: Hi everyone! Have anyone used the Lennard-Jones 9-6 potential for coarse-grained models? when I use it, I get a very different result from that is got from the same Lennard-Jones 9-6 potential formed a potential table,the latter's results are comparable to the experiments. when I use LJ-9-6 potential,the ITP file is as following: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 9 Even if this may generate the correct parameters (please use gmxdump to check your tpr file) you still have to provide a user table to mdrun and to set vdw-type = user in your mdp file. You may need to change the nbfunc to three as well. Check source code in src/kernel/convparm to see what is going on. I don't think this is documented anywhere, is it? Thanks very much for your advice! According to you , I provide a user table( Does this mean that LJ'parameters epsilon and sigma setted in the ITP file don't work ? ) and set vdw-type = user as well as change nbfunc to three ,but grompp reports some errors that : Invalid nonbond function selector '3' using LJ,I read the manual again,it says : non-bond type =1(Lennaed-Jones) or 2(Buckingham), that is seemed that 3 is a illegal choice, is there something wrong? [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon opls_001 Cx 6 78.01900A0.505 2.95; [ moleculetype ] ; Name nrexcl Phenyl 1 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_001 1 Phenyl C1 10.000 78.0190 other files ,such as mdp file and top file ,are all the same as normal LJ-12-6 potential, are these correct if I want to use LJ-9-6 potential? Do I still need to change something? Thanks very much for your kindness! ´©Ã½µÃÃð´ø ¼ÃÃîãë´¨µÃÃðûÃÃÃê http://512.mail.163.com/mailstamp/stamp/dz/activity.do?from=footer ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe
Re: [gmx-users] Shared library version binary on CYGWIN
On Wed, 2009-05-27 at 15:05 +0900, Makoto Yoneya wrote: I found the libtool within gromacs source (both 3.3.3 and 4.0.4) is not as new as that of e.g. fftw-3.2.1 (which use the libtool-2.2.6). I'm wondering if the libtool version was updated to the newer one, then the DLLs could be generated properly, because fftw-3.2.1 can build DLL on cygwin if it configured with --enable-shared. I'd tried that with gromacs a little but no success as I have no detailed knowledge on GNU autotools. You can of course try $ autoreconf -f which regenerates the build scripts and updates libtool and compiling with $ configure --enable-shared --disable-static after that. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Strange assignment of atoms to processors with pd
Hi, I'm simulating non-periodic systems in vacuo, using constrained h-bonds and particle decomposition. For some of my simulations the cpu-usage seem far from optimal. The first cpu gets no atoms, while the second one gets plenty and the remaining cpus get less than I expected. Is this a bug? An excerpt from the log file: There are: 2911 Atoms There are: 317 VSites splitting topology... There are 999 charge group borders and 318 shake borders There are 318 total borders Division over nodes in atoms: 0 1960 212 212 212 212 212 208 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= -1, targetcg= 499, myshift= 1 CPU= 1, lastcg= 681, targetcg= 182, myshift= 0 CPU= 2, lastcg= 734, targetcg= 235, myshift= 7 CPU= 3, lastcg= 787, targetcg= 288, myshift= 6 CPU= 4, lastcg= 840, targetcg= 341, myshift= 5 CPU= 5, lastcg= 893, targetcg= 394, myshift= 4 CPU= 6, lastcg= 946, targetcg= 447, myshift= 3 CPU= 7, lastcg= 998, targetcg= 499, myshift= 2 pd-shift = 7, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 Workload division nnodes: 8 pd-shift: 7 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 0 0 0 0 1 0 1960 0 682 2 1960 212 682 53 3 2172 212 735 53 4 2384 212 788 53 5 2596 212 841 53 6 2808 212 894 53 7 3020 208 947 52 … Total Scaling: 18% of max performance -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Strange assignment of atoms to processors with pd
I should add that this problem only seem to arise when the analyte is covered with a thin sheet of water. When simulating a dry analyte I get good scaling. In the latter case the charges, and therefore the topology, is slightly different. /Erik Erik Marklund skrev: Hi, I'm simulating non-periodic systems in vacuo, using constrained h-bonds and particle decomposition. For some of my simulations the cpu-usage seem far from optimal. The first cpu gets no atoms, while the second one gets plenty and the remaining cpus get less than I expected. Is this a bug? An excerpt from the log file: There are: 2911 Atoms There are: 317 VSites splitting topology... There are 999 charge group borders and 318 shake borders There are 318 total borders Division over nodes in atoms: 0 1960 212 212 212 212 212 208 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= -1, targetcg= 499, myshift= 1 CPU= 1, lastcg= 681, targetcg= 182, myshift= 0 CPU= 2, lastcg= 734, targetcg= 235, myshift= 7 CPU= 3, lastcg= 787, targetcg= 288, myshift= 6 CPU= 4, lastcg= 840, targetcg= 341, myshift= 5 CPU= 5, lastcg= 893, targetcg= 394, myshift= 4 CPU= 6, lastcg= 946, targetcg= 447, myshift= 3 CPU= 7, lastcg= 998, targetcg= 499, myshift= 2 pd-shift = 7, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 Workload division nnodes: 8 pd-shift: 7 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 0 0 0 0 1 0 1960 0 682 2 1960 212 682 53 3 2172 212 735 53 4 2384 212 788 53 5 2596 212 841 53 6 2808 212 894 53 7 3020 208 947 52 … Total Scaling: 18% of max performance -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] gmxtest
Hi Mark, Thanks! S. On Wed, May 27, 2009 at 12:03 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Mark Abraham wrote: Simba Xiao wrote: Dear all, Does your GMX 4 past the gmxtest package in the gmx wiki ? My Gromacs 4.0.4 can not pass all the test. The test tip4p, ti4pflex and some kernel issues failed. That's normal at the moment, unfortunately. Future releases of gmxtest will probably fix the non-kernel issues, and GROMACS 4.0.5 will fix the kernel issues. Sorry, I mis-remembered something. The kernel issues were caused by a hard-to-provoke bug in 3.3.x which provided the reference trajectories. GROMACS 4.0.x are fine, but the test fails because of the flawed reference values. See bugzilla 313 for details. Mark I use standard packages and everything looks find. The simulation result are good and identical to gromacs 3.3.3. But, still it annoys me with the test result. Can somebody tell how much the test matters and can somebody tell something more than the wiki tells (It dose not explain much). Well, it does explain things, but not such that a new GROMACS user can get a useful result from existing versions of gmxtest. I'll upgrade the wiki documentation if/when a gmxtest re-release happens. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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 -- Sen PICB, Shanghai, 200031 CHINA ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Strange assignment of atoms to processors with pd
Erik Marklund wrote: I should add that this problem only seem to arise when the analyte is covered with a thin sheet of water. When simulating a dry analyte I get good scaling. In the latter case the charges, and therefore the topology, is slightly different. How about vsites? Did you happen to turn them off as well in the vacuum case? /Erik Erik Marklund skrev: Hi, I'm simulating non-periodic systems in vacuo, using constrained h-bonds and particle decomposition. For some of my simulations the cpu-usage seem far from optimal. The first cpu gets no atoms, while the second one gets plenty and the remaining cpus get less than I expected. Is this a bug? An excerpt from the log file: There are: 2911 Atoms There are: 317 VSites splitting topology... There are 999 charge group borders and 318 shake borders There are 318 total borders Division over nodes in atoms: 0 1960 212 212 212 212 212 208 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= -1, targetcg= 499, myshift= 1 CPU= 1, lastcg= 681, targetcg= 182, myshift= 0 CPU= 2, lastcg= 734, targetcg= 235, myshift= 7 CPU= 3, lastcg= 787, targetcg= 288, myshift= 6 CPU= 4, lastcg= 840, targetcg= 341, myshift= 5 CPU= 5, lastcg= 893, targetcg= 394, myshift= 4 CPU= 6, lastcg= 946, targetcg= 447, myshift= 3 CPU= 7, lastcg= 998, targetcg= 499, myshift= 2 pd-shift = 7, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 Workload division nnodes: 8 pd-shift: 7 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 0 0 0 0 1 0 1960 0 682 2 1960 212 682 53 3 2172 212 735 53 4 2384 212 788 53 5 2596 212 841 53 6 2808 212 894 53 7 3020 208 947 52 … Total Scaling: 18% of max performance -- 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://www.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] Normal Mode Analysis
Hi,
I don't know exactly what went wrong when I tried to patch the file. There
was a on line 18 in the fix file, actually. I checked it. With the file
you sent me, gmxdump works fine.
Thank you very much for your help.
Best regards, Franzi
---
Franziska Hoffgaard
PhD Student
Bioinformatics Theo. Biology Group
TU Darmstadt
2009/5/26 Berk Hess g...@hotmail.com
Hi,
But there is a '' on line 18, at least in my mail.
I tested the patch and it worked for me.
Maybe something went wrong when cut and pasting the patch from the email?
I can mail you the whole file personally tomorrow, if required.
Berk
--
Date: Tue, 26 May 2009 14:47:52 +0200
Subject: Re: [gmx-users] Normal Mode Analysis
From: f.hoffga...@gmail.com
To: gmx-users@gromacs.org
Hi
thanks for your reply. I tried patching as you described it, but I got the
error message:
patch: `' expected at line 18 of patch
Franzi
---
Franziska Hoffgaard
PhD Student
Bioinformatics Theo. Biology Group
TU Darmstadt
2009/5/26 Berk Hess g...@hotmail.com
Hi,
I just saw that 4.0 uses a new mtx format which can also efficiently store
sparse matrices.
Please try if my modified gmxdump for 4.0.5 works?
Store the data below in a file called fix and then do:
patch gmxdump.c fix
Berk
61a62,63
#include sparsematrix.h
#include mtxio.h
364a367,402
static void list_mtx(char *fn)
{
int nrow,ncol,i,j,k;
real *full=NULL,value;
gmx_sparsematrix_t * sparse=NULL;
gmx_mtxio_read(fn,nrow,ncol,full,sparse);
if (full == NULL) {
snew(full,nrow*ncol);
for(i=0;inrow*ncol;i++) {
full[i] = 0;
}
for(i=0;isparse-nrow;i++) {
for(j=0;jsparse-ndata[i];j++) {
k = sparse-data[i][j].col;
value = sparse-data[i][j].value;
full[i*ncol+k] = value;
full[k*ncol+i] = value;
}
}
gmx_sparsematrix_destroy(sparse);
}
printf(%d %d\n,nrow,ncol);
for(i=0; inrow; i++) {
for(j=0; jncol; j++) {
printf( %g,full[i*ncol+j]);
}
printf(\n);
}
sfree(full);
}
381a420
{ efMTX, -mtx, hessian, ffOPTRD },
409a449,450
else if (ftp2bSet(efMTX,NFILE,fnm))
list_mtx(ftp2fn(efMTX,NFILE,fnm));
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Re: [gmx-users] Strange assignment of atoms to processors with pd
David van der Spoel skrev: Erik Marklund wrote: I should add that this problem only seem to arise when the analyte is covered with a thin sheet of water. When simulating a dry analyte I get good scaling. In the latter case the charges, and therefore the topology, is slightly different. How about vsites? Did you happen to turn them off as well in the vacuum case? Turned off in all cases. The VSites mentioned in the log file is the 4:th particle on the tip4p-water molecules. /Erik Erik Marklund skrev: Hi, I'm simulating non-periodic systems in vacuo, using constrained h-bonds and particle decomposition. For some of my simulations the cpu-usage seem far from optimal. The first cpu gets no atoms, while the second one gets plenty and the remaining cpus get less than I expected. Is this a bug? An excerpt from the log file: There are: 2911 Atoms There are: 317 VSites splitting topology... There are 999 charge group borders and 318 shake borders There are 318 total borders Division over nodes in atoms: 0 1960 212 212 212 212 212 208 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= -1, targetcg= 499, myshift= 1 CPU= 1, lastcg= 681, targetcg= 182, myshift= 0 CPU= 2, lastcg= 734, targetcg= 235, myshift= 7 CPU= 3, lastcg= 787, targetcg= 288, myshift= 6 CPU= 4, lastcg= 840, targetcg= 341, myshift= 5 CPU= 5, lastcg= 893, targetcg= 394, myshift= 4 CPU= 6, lastcg= 946, targetcg= 447, myshift= 3 CPU= 7, lastcg= 998, targetcg= 499, myshift= 2 pd-shift = 7, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 Workload division nnodes: 8 pd-shift: 7 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 0 0 0 0 1 0 1960 0 682 2 1960 212 682 53 3 2172 212 735 53 4 2384 212 788 53 5 2596 212 841 53 6 2808 212 894 53 7 3020 208 947 52 … Total Scaling: 18% of max performance -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Twin range cut-off's: rlist and rvdw
Dear Gromacs users, I have a question about the twin range cut-off's in Gromacs. If I choose vdwtype as Cut-off, the manual on run parameters tells me that I need to choose rvdw=rlist in this case. I have read the section on the treatment of cutoffs in the manual and also the mailing list. My understanding on the twin range cut-off's is following: 1, Every nstlist steps, the neighborlist is updated according to the cut-off of neighborlist rlist and all interactions are calculated according to the cut-off of forces, such as rvdw; 2, Every step, all interactions of atom pairs in the neighborlist are calculated. If my understanding above is correct, it seems that the concept or the algorithm of neighborlist for the twin range cut-off's in Gromacs is different from the original concept of Verlet neighborlist which is discussed in the textbook on MD simulations, for instance, in the book Understanding Molecular Simulation by Frenkel and Smit. The original algorithm of Verlet list needs rlistrvdw in order to contain all particles which might have interactions. However, the twin range cut-off's in Gromacs with rvdw=rlist seems to be contradict to this original idea of Verlet list and to miss some contribution to the interaction by the particles which stay between rlist and rvdw in the normal steps without updating the neighborlist. So my question is: what is the idea for Gromacs to take such algorithm of twin range cut-off's? Thanks! Yan ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Strange assignment of atoms to processors with pd
Erik Marklund wrote: David van der Spoel skrev: Erik Marklund wrote: I should add that this problem only seem to arise when the analyte is covered with a thin sheet of water. When simulating a dry analyte I get good scaling. In the latter case the charges, and therefore the topology, is slightly different. How about vsites? Did you happen to turn them off as well in the vacuum case? Turned off in all cases. The VSites mentioned in the log file is the 4:th particle on the tip4p-water molecules. OK. Did you try a one step run with -debug? It may give more info on the partitioning. /Erik Erik Marklund skrev: Hi, I'm simulating non-periodic systems in vacuo, using constrained h-bonds and particle decomposition. For some of my simulations the cpu-usage seem far from optimal. The first cpu gets no atoms, while the second one gets plenty and the remaining cpus get less than I expected. Is this a bug? An excerpt from the log file: There are: 2911 Atoms There are: 317 VSites splitting topology... There are 999 charge group borders and 318 shake borders There are 318 total borders Division over nodes in atoms: 0 1960 212 212 212 212 212 208 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= -1, targetcg= 499, myshift= 1 CPU= 1, lastcg= 681, targetcg= 182, myshift= 0 CPU= 2, lastcg= 734, targetcg= 235, myshift= 7 CPU= 3, lastcg= 787, targetcg= 288, myshift= 6 CPU= 4, lastcg= 840, targetcg= 341, myshift= 5 CPU= 5, lastcg= 893, targetcg= 394, myshift= 4 CPU= 6, lastcg= 946, targetcg= 447, myshift= 3 CPU= 7, lastcg= 998, targetcg= 499, myshift= 2 pd-shift = 7, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 Workload division nnodes: 8 pd-shift: 7 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 0 0 0 0 1 0 1960 0 682 2 1960 212 682 53 3 2172 212 735 53 4 2384 212 788 53 5 2596 212 841 53 6 2808 212 894 53 7 3020 208 947 52 … Total Scaling: 18% of max performance -- 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://www.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] Strange assignment of atoms to processors with pd
Hi, This is plain 4.0 code is presume? This problem should be fixed then. But I now also made vacuum without cut-off working with domain decomposition in CVS head. Compared to a not-unbalanced PD (for instance only a protein, no water) DD is slightly slower. But DD will be faster than a badly balanced PD system. Berk Date: Wed, 27 May 2009 11:04:49 +0200 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] Strange assignment of atoms to processors with pd Erik Marklund wrote: David van der Spoel skrev: Erik Marklund wrote: I should add that this problem only seem to arise when the analyte is covered with a thin sheet of water. When simulating a dry analyte I get good scaling. In the latter case the charges, and therefore the topology, is slightly different. How about vsites? Did you happen to turn them off as well in the vacuum case? Turned off in all cases. The VSites mentioned in the log file is the 4:th particle on the tip4p-water molecules. OK. Did you try a one step run with -debug? It may give more info on the partitioning. /Erik Erik Marklund skrev: Hi, I'm simulating non-periodic systems in vacuo, using constrained h-bonds and particle decomposition. For some of my simulations the cpu-usage seem far from optimal. The first cpu gets no atoms, while the second one gets plenty and the remaining cpus get less than I expected. Is this a bug? An excerpt from the log file: There are: 2911 Atoms There are: 317 VSites splitting topology... There are 999 charge group borders and 318 shake borders There are 318 total borders Division over nodes in atoms: 0 1960 212 212 212 212 212 208 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= -1, targetcg= 499, myshift= 1 CPU= 1, lastcg= 681, targetcg= 182, myshift= 0 CPU= 2, lastcg= 734, targetcg= 235, myshift= 7 CPU= 3, lastcg= 787, targetcg= 288, myshift= 6 CPU= 4, lastcg= 840, targetcg= 341, myshift= 5 CPU= 5, lastcg= 893, targetcg= 394, myshift= 4 CPU= 6, lastcg= 946, targetcg= 447, myshift= 3 CPU= 7, lastcg= 998, targetcg= 499, myshift= 2 pd-shift = 7, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 Workload division nnodes: 8 pd-shift: 7 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 0 0 0 0 1 0 1960 0 682 2 1960 212 682 53 3 2172 212 735 53 4 2384 212 788 53 5 2596 212 841 53 6 2808 212 894 53 7 3020 208 947 52 … Total Scaling: 18% of max performance -- 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.se sp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Strange assignment of atoms to processors with pd
This was done with verision 4.0.4, taken straight from the website. I've already simulated a great deal with this version and I'd hate to swap versions in the middle of the project. As for the -debug runs, I did it for the dry analyte and for one with a 6 Å water layer. It seems that the protein is indeed divided over the processors if no other molecules are present. When there are other molecules, such as water, in the system then I suspect that the molecules are divided over the processors. This doesn't explain why the first processor got no atoms when I ran the simulations on 8 cpus though. without water ===-, There are: 1960 Atoms splitting topology... There are 698 charge group borders and 1 shake borders There are 698 total borders Division over nodes in atoms: 492 489 488 491 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= 171, targetcg= 520, myshift=2 CPU= 1, lastcg= 354, targetcg=6, myshift=3 CPU= 2, lastcg= 521, targetcg= 172, myshift=2 CPU= 3, lastcg= 697, targetcg= 348, myshift=2 pd-shift = 3, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 BONDS 259 263 250 253 ANGLES 894 867 901 870 PDIHS 110 11787 107 RBDIHS1002 967 1015 960 LJ14 1289 1260 1318 1234 CONSTR 242 232 244 241 Workload division nnodes: 4 pd-shift:3 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 0 492 0 172 1 492 489 172 183 2 981 488 355 167 31469 491 522 176 ===-' == with a bit of water ===-, There are: 5086 Atoms There are: 1042 VSites splitting topology... There are 1724 charge group borders and 1043 shake borders There are 1043 total borders Division over nodes in atoms: 1960138813921388 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= 681, targetcg= 1543, myshift=3 CPU= 1, lastcg= 1028, targetcg= 166, myshift=3 CPU= 2, lastcg= 1376, targetcg= 514, myshift=2 CPU= 3, lastcg= 1723, targetcg= 862, myshift=2 pd-shift = 3, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 BONDS 1025 0 0 0 ANGLES3547 0 0 0 PDIHS 426 0 0 0 RBDIHS3950 0 0 0 LJ14 5106 0 0 0 CONSTR 959 0 0 0 Workload division nnodes: 4 pd-shift:3 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 01960 0 682 119601388 682 347 2334813921029 348 3474013881377 347 Berk Hess skrev: Hi, This is plain 4.0 code is presume? This problem should be fixed then. But I now also made vacuum without cut-off working with domain decomposition in CVS head. Compared to a not-unbalanced PD (for instance only a protein, no water) DD is slightly slower. But DD will be faster than a badly balanced PD system. Berk Date: Wed, 27 May 2009 11:04:49 +0200 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] Strange assignment of atoms to processors with pd Erik Marklund wrote: David van der Spoel skrev: Erik Marklund wrote: I should add that this problem only seem to arise when the analyte is covered with a thin sheet of water. When simulating a dry analyte I get good scaling. In the latter case the charges, and therefore the topology, is slightly different. How about vsites? Did you happen to turn them off as well in the vacuum case? Turned off in all cases. The VSites mentioned in the log file is the 4:th particle on the tip4p-water molecules. OK. Did you try a one step run with -debug? It may give more info on the partitioning. /Erik Erik Marklund skrev: Hi, I'm simulating non-periodic systems in vacuo, using constrained h-bonds and particle decomposition. For some of my simulations the cpu-usage seem far from optimal. The first cpu gets no atoms, while the second one gets plenty and the remaining cpus get less than I expected. Is this a bug? An excerpt from the log file: There are: 2911 Atoms There are: 317 VSites splitting topology... There are 999 charge group borders and 318 shake borders There are 318 total borders Division over nodes in atoms: 0 1960 212 212 212 212 212 208 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= -1, targetcg= 499, myshift= 1 CPU= 1, lastcg= 681, targetcg= 182, myshift= 0 CPU= 2, lastcg= 734, targetcg= 235, myshift= 7 CPU= 3, lastcg= 787, targetcg= 288, myshift= 6 CPU= 4, lastcg= 840, targetcg= 341, myshift= 5 CPU= 5, lastcg= 893, targetcg= 394, myshift= 4 CPU= 6,
[gmx-users] Packages for building topologies
Hi All, I was doing some MD simulation over the docked complex and following the drug-enzyme tutorial for the same. The tutorial provided by Kerrigan's is really helpful. Only problem with the tutorial is generating topologies, for which PRODRG server is suggested. I want to use some stand alone package for generating the topologies which can run on local machine. Does anybody have idea of such packages ? Suggest me any other alternate of generating topologies. With thanks in advance.. ~Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Packages for building topologies
vivek sharma wrote: Hi All, I was doing some MD simulation over the docked complex and following the drug-enzyme tutorial for the same. The tutorial provided by Kerrigan's is really helpful. Only problem with the tutorial is generating topologies, for which PRODRG server is suggested. I want to use some stand alone package for generating the topologies which can run on local machine. Does anybody have idea of such packages ? There are several within the Users Contributions section of the website, but then you are generally limited to whatever force field the authors of those programs decided to use. If you want a standalone copy of PRODRG, you can request one by clicking How to obtain at the top of the PRODRG site. -Justin Suggest me any other alternate of generating topologies. With thanks in advance.. ~Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] structure factor using g_rdf: grid option does not work
Hi,
I was trying to get the static structure factor using the following
command line:
g_rdf -f trr filename -s tpr filename -sq -b 15000 -e 2 -endq 0.5
The output sq.xvg came as follows:
0.0 0.0
0.0861717775.32914
0.1723317292.77243
0.2585016632.64157
0.3446615728.30566
0.4308314588.50674
It seems the grid was automatically set to 0.08617 nm^{-1}. But when I
tried to lower it by manually specifying the grid option as follows:
g_rdf -f trr filename -s tpr filename -sq -b 15000 -e 2 -endq
0.5 -grid 0.01
even then the output remains unchanged:
0.0 0.0
0.0861717775.32914
0.1723317292.77243
0.2585016632.64157
0.3446615728.30566
0.4308314588.50674
Please tell me where I am going wrong. The manual talks about the -grid
option, but that doesn't seem to work somehow! How do I make it work?
Thanks,
Suman.
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Re: [gmx-users] Twin range cut-off's: rlist and rvdw
On Wed, 2009-05-27 at 11:00 +0200, Yan Chai wrote: If my understanding above is correct, it seems that the concept or the algorithm of neighborlist for the twin range cut-off's in Gromacs is different from the original concept of Verlet neighborlist which is discussed in the textbook on MD simulations, for instance, in the book Understanding Molecular Simulation by Frenkel and Smit. The original algorithm of Verlet list needs rlistrvdw in order to contain all particles which might have interactions. However, the twin range cut-off's in Gromacs with rvdw=rlist seems to be contradict to this original idea of Verlet list and to miss some contribution to the interaction by the particles which stay between rlist and rvdw in the normal steps without updating the neighborlist. So my question is: what is the idea for Gromacs to take such algorithm of twin range cut-off's? In the twin range method [1] interactions that are in the range rlist..rvdw are only calculated during neighborlist updates. In the mean time they are considered to stay constant. The idea behind this is that when rrlist the interactions are weaker and also vary more slowly, thus one doesn't need to be as precise in taking those interactions into account. [1] http://dx.doi.org/10.1002/prot.340060203 -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Ac-CoA topology problem
Hi gmx-users, I am a new user of gromacs. I am trying to simulate a protein with cofactor Acetyl-CoA. I have generated gromacs topology for cofactor using prodrg server. I used OPLS-AA force field. I got the error message Fatal error: Atomtype OA not found. I couldn't fix this problem. Could any one suggest me how to fix this problem. Thanks in advance, Yours sincerely, S. Thamotharan ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Ac-CoA topology problem
Thamu wrote: Hi gmx-users, I am a new user of gromacs. I am trying to simulate a protein with cofactor Acetyl-CoA. I have generated gromacs topology for cofactor using prodrg server. I used OPLS-AA force field. I got the error message Fatal error: Atomtype OA not found. PRODRG generates Gromos-compatible force field parameters, not OPLS. -Justin I couldn't fix this problem. Could any one suggest me how to fix this problem. Thanks in advance, Yours sincerely, S. Thamotharan ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] Twin range cut-off's: rlist and rvdw
On Wed, 2009-05-27 at 14:33 +0200, Yan Chai wrote: It seems that in the twin range cut-off method, rlist does not only play a role as a cut-off for neighbor searching, but also as a cut-off for short-range interactions. Do I understand correctly? If you're using Coulombic cutoffs, then yes. If you're using PME, then AFAIK the part r rcut will be performed in Fourier space. Do people think the effect of these inward moving and outward moving particles is small and the error for calculation can be tolerated? When particles move in and out of the cutoff range it induces static in the properties. Ideally for monocomponent systems (such as metals) the cutoff should be in an (absolute) minimum of the pair correlation function, i.e. there aren't many particles in the region where the cutoff is made. For molecular systems the decision of a cutoff is harder, since some pair correlations stay quite constant and there is no clear cut way to make the decision. The farther you go the fewer static you get. Roughly speaking, the number of particles at cutoff range grows as r_cut^2, but for Lennard-Jones the interaction weakens as r_cut^-6, resulting in an error proportional to r_cut^-4. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Twin range cut-off's: rlist and rvdw
Hi, I don't think it matters much if you put the cut-off at a minimum in the rdf. The real issue is that the force is not updated beyond the cut-off, while the atoms there still move. You want as little motion, of better as little change in force due to the motion of the atoms as possible. The solution to this is to increase the cut-off as much as possible, but this is computationally unfavourable. I should also note the all versions of Gromacs up till now use a very simplistic twin-cut off setup with an integrator which is not reversible. This can lead to significant energy increase in the system. Therefore twin-range cut-off should not be used for Coulomb interactions, only for Lennard-Jones, where the forces are anyhow very small. We might consider implementing a proper multiple time step integrator for version 4.1 or 4.2. Berk Subject: Re: [gmx-users] Twin range cut-off's: rlist and rvdw From: jussi.leht...@helsinki.fi To: gmx-users@gromacs.org Date: Wed, 27 May 2009 16:05:25 +0300 On Wed, 2009-05-27 at 14:33 +0200, Yan Chai wrote: It seems that in the twin range cut-off method, rlist does not only play a role as a cut-off for neighbor searching, but also as a cut-off for short-range interactions. Do I understand correctly? If you're using Coulombic cutoffs, then yes. If you're using PME, then AFAIK the part r rcut will be performed in Fourier space. Do people think the effect of these inward moving and outward moving particles is small and the error for calculation can be tolerated? When particles move in and out of the cutoff range it induces static in the properties. Ideally for monocomponent systems (such as metals) the cutoff should be in an (absolute) minimum of the pair correlation function, i.e. there aren't many particles in the region where the cutoff is made. For molecular systems the decision of a cutoff is harder, since some pair correlations stay quite constant and there is no clear cut way to make the decision. The farther you go the fewer static you get. Roughly speaking, the number of particles at cutoff range grows as r_cut^2, but for Lennard-Jones the interaction weakens as r_cut^-6, resulting in an error proportional to r_cut^-4. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] Twin range cut-off's: rlist and rvdw
On Wed, May 27, 2009 at 3:05 PM, Jussi Lehtola jussi.leht...@helsinki.fiwrote: On Wed, 2009-05-27 at 14:33 +0200, Yan Chai wrote: It seems that in the twin range cut-off method, rlist does not only play a role as a cut-off for neighbor searching, but also as a cut-off for short-range interactions. Do I understand correctly? If you're using Coulombic cutoffs, then yes. If you're using PME, then AFAIK the part r rcut will be performed in Fourier space. Excuse me, to make sure whether my understanding is correct or not, might I check the following two examples? Case 1, let's consider PME and set rlist=rcoulomb. At time t=0, there are a particle O at the original point, a outward moving particle A within the radius of rlist=rcoulomb, and a inward moving particle B out of the radius of rlist=rcoulomb, as shown below O -- A -- rlist -- B, for t=0 I set nstlist=10. At t=0, the neighborlist of particle O is created and particle A is on the list but particle B is not. The Coulomb forces on particle O is also calculated, and F_OA is calculated in real space while F_OB is calculated in Fourier space: Fcoulomb=Fcoulomb_OA_real+Fcoulomb_OB_fourier, for t=0. Let's imagine when the time is between t=0 and t=10, before the second time for neighborlist update, particle A moves outside of the radius of rlist=rcoulomb and particle B moves inside of the radius of rlist=rcoulomb, as shown below O -- B -- rlist -- A, for 0tnstlist Now particle A is still on the neighborlist of particle O and particle B is still not. I would expect that Gromacs will calculate the Coulomb interaction to particle O by particle A twice: once in the real space because particle A is on the neighborlist of particle O, and the other one at the same time in Fourier space because particle is outside of the radius rcoulomb. On the other hand, there will be no account for the Coulomb interaction to particle O by particle B because particle B is neither on the list of O nor outside of rcoulomb. Fcoulomb=Fcoulomb_OA_real+Fcoulomb_OA_fourier, for 0tnstlist. Case 2, let's consider van der Waals interaction and set rlistrvdw. Similar to Case 1, we have particles which shift the positions as below: O -- A -- rlist -- B -- rvdw, for t=0 O -- B -- rlist -- A -- rvdw, for 0tnstlist I would expect that during 0tnstlist, the van der Waals force applied on particle O will be Fvdw=Fvdw_OA(0tnstlist)+Fvdw_OB(t=0), for 0tnstlist which means that particle A can apply van der Waals force on particle O even if particle A is beyond rlist since particle A is still on the neighborlist of particle O. Do I understand correctly for these two cases above? Thanks! Yan ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Viscosity using periodic perturbation method
Dear Berk: Thank you so much for your help! I read your paper: Determing the shear viscosity of model liquids from molecular dynamics simulations You used NVT? My question is which one is better? NPT or NVT? Strictly speaking it might be incorrect, but since pressure scaling is usually less than 1% it will not affect your results significantly. So technically we should use NVT for the periodic perturbation method, right? Thanks! On Tue, May 26, 2009 at 12:03 AM, Berk Hess g...@hotmail.com wrote: Hi, Yes, you can use NPT, the code takes care of this properly. Strictly speaking it might be incorrect, but since pressure scaling is usually less than 1% it will not affect your results significantly. Berk. -- Date: Mon, 25 May 2009 15:19:10 -0700 From: yson...@asu.edu To: gmx-users@gromacs.org Subject: [gmx-users] Viscosity using periodic perturbation method Dear users: I was trying to calculate the viscosity of liquid system using periodic perturbation method. Does this method require NVT ensemble simulation in stead of NPT ? Because I read some literature on periodic perturbation method. they all used NVT. I did not found any information about this on the manual. Can I use NPT Non-equilibrium MD in order to use periodic perturbation method? Thanks in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- Express yourself instantly with MSN Messenger! MSN Messengerhttp://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://www.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: solution molecules cannot be set by mdrun after neutralization
My integrator is steep, which should perform EM. This is my mdp file: title = 4AKE_PREMsteep cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = all-bonds integrator = steep nsteps = 500 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 DispCorr = no ; ; Energy minimizing stuff ; emtol = 1.0 emstep = 0.01 I learnt from the tutorials (s-peptide) that in order to do a position restrained MD the I have to set the constraints (all-bonds in this case). Is that incorrect? Is it valid for EM as well? Thank you for your advice, Stefano. Mark Abraham ha scritto: Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Yes. You're not doing EM. t = 0.011 ps: is a big clue. Choose your integrator in your .mdp file better. Also, as Justin suggests, please be careful with the constraint/restraint terminology. Mark Thanks, Stefano. Stefano Meliga ha scritto: Hi everybody, I neutralized my system with the commands: $grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p 4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr $grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname CL- (adding the atoms to the solution SOL) I renamed the files to keep track of the different topology files: mv 4AKEallHsol_pre.top 4AKEallHion.top mv #4AKEallHsol_pre.top.1# 4AKEallHsol_pre.top I run an all-bonds position restraint steepest descent EM: $grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c 4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o 4AKEallHion.tpr $grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c 4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v mdrun exits successfully but displays the warning: t = 0.011 ps: Water molecule starting at atom 17223 can not be settled. Check for bad contacts and/or reduce the timestep. In the gro file atom 17223 is an oxigen of the solution Going further with my simulation i run a all-bonds position restrained conjugate gradient EM: $grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c 4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top -o 4AKEallH_PREMsteep.tpr $grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c 4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v but get the fatal error: Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (2200) And some of this warnings are again solution's molecules that cannot be set. May the problem be related to the ions added to neutralise the system? mdrun was not showing this problem with the non-neutral system in input. Thanks a lot, Stefano ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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://www.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: solution molecules cannot be set by mdrun after neutralization
Stefano Meliga wrote: My integrator is steep, which should perform EM. This is my mdp file: title = 4AKE_PREMsteep cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = all-bonds integrator = steep nsteps = 500 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 DispCorr = no ; ; Energy minimizing stuff ; emtol = 1.0 emstep = 0.01 I learnt from the tutorials (s-peptide) that in order to do a position restrained MD the I have to set the constraints (all-bonds in this case). Is that incorrect? Is it valid for EM as well? Position restraints != bond contraints. Using constraints = all-bonds will constrain the bond lengths, but not restrain the positions of the atoms. If you want to do position-restrained MD, you have to define = -DPOSRES (according to the #ifdef POSRES block in the topology, assuming you made one automatically from pdb2gmx). Using position restraints in EM doesn't serve much of a purpose in my mind, unless you really need to preserve the exact initial configuration; it may in fact prevent your system from converging if some bad geometry is being held in place. -Justin Thank you for your advice, Stefano. Mark Abraham ha scritto: Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Yes. You're not doing EM. t = 0.011 ps: is a big clue. Choose your integrator in your .mdp file better. Also, as Justin suggests, please be careful with the constraint/restraint terminology. Mark Thanks, Stefano. Stefano Meliga ha scritto: Hi everybody, I neutralized my system with the commands: $grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p 4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr $grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname CL- (adding the atoms to the solution SOL) I renamed the files to keep track of the different topology files: mv 4AKEallHsol_pre.top 4AKEallHion.top mv #4AKEallHsol_pre.top.1# 4AKEallHsol_pre.top I run an all-bonds position restraint steepest descent EM: $grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c 4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o 4AKEallHion.tpr $grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c 4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v mdrun exits successfully but displays the warning: t = 0.011 ps: Water molecule starting at atom 17223 can not be settled. Check for bad contacts and/or reduce the timestep. In the gro file atom 17223 is an oxigen of the solution Going further with my simulation i run a all-bonds position restrained conjugate gradient EM: $grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c 4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top -o 4AKEallH_PREMsteep.tpr $grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c 4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v but get the fatal error: Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (2200) And some of this warnings are again solution's molecules that cannot be set. May the problem be related to the ions added to neutralise the system? mdrun was not showing this problem with the non-neutral system in input. Thanks a lot, Stefano ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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://www.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] mpi problem during installation
HI all, I am trying to compile GROMACS 4.0.5 on my mac (10.5) using './configure --enable-mpi --disable-float --with-fft=no make -j2 make install'. I installed on the system lam 7.0.6 './configure make make install'. The error message I get is: mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -framework Accelerate -o grompp grompp.o ./.libs/libgmxpreprocess_mpi_d.a -L/usr/X11/lib ../mdlib/.libs/libmd_mpi_d.a /Users/ikass/Downloads/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a /usr/lib/libxml2.dylib -lpthread -lz -licucore -lm /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/libXdmcp.6.0.0.dylib Undefined symbols: _lam_mpi_sum, referenced from: _lam_mpi_sum$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_sum$non_lazy_ptr in libmd_mpi_d.a(domdec.o) _lam_mpi_sum$non_lazy_ptr in libmd_mpi_d.a(gmx_wallcycle.o) _lam_mpi_sum$non_lazy_ptr in libmd_mpi_d.a(pme.o) _lam_mpi_comm_world, referenced from: _lam_mpi_comm_world$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_comm_world$non_lazy_ptr in libgmx_mpi_d.a(main.o) _lam_mpi_float, referenced from: _lam_mpi_float$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_double, referenced from: _lam_mpi_double$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(partdec.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(gmx_wallcycle.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(pme.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(gmx_parallel_3dfft.o) _lam_mpi_byte, referenced from: _lam_mpi_byte$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(partdec.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(domdec.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(domdec_network.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(pme_pp.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(sim_util.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(pme.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(stat.o) _lam_mpi_int, referenced from: _lam_mpi_int$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_int$non_lazy_ptr in libmd_mpi_d.a(domdec.o) _lam_mpi_int$non_lazy_ptr in libmd_mpi_d.a(pme.o) ld: symbol(s) not found collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 Any ideas? ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Question about g_cluster
I recently started using g_cluster and have a question. When I run g_cluster, the program asks me to select two groups. The output looks something like this: Select group for least squares fit and RMSD calculation: Group 0 ( C-alpha) has 383 elements Group 1 ( active_site) has 2438 elements Select a group: 0 Select group for output: Group 0 ( C-alpha) has 383 elements Group 1 ( active_site) has 2438 elements Select a group: 1 I have assumed that g_cluster aligns the trajectory by the first group selected, and then clusters based on the second group. Recently, however, someone told me that both the alignment and the clustering is performed only on the first group. Can anyone confirm this? If so, what's the purpose of the second group? Thanks, Jacob ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] mpi problem during installation
Itamar Kass wrote: HI all, I am trying to compile GROMACS 4.0.5 on my mac (10.5) using './configure --enable-mpi --disable-float --with-fft=no make -j2 make install'. I installed on the system lam 7.0.6 './configure make make install'. The error message I get is: mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -framework Accelerate -o grompp grompp.o ./.libs/libgmxpreprocess_mpi_d.a -L/usr/X11/lib ../mdlib/.libs/libmd_mpi_d.a /Users/ikass/Downloads/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a /usr/lib/libxml2.dylib -lpthread -lz -licucore -lm /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/libXdmcp.6.0.0.dylib Undefined symbols: _lam_mpi_sum, referenced from: _lam_mpi_sum$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_sum$non_lazy_ptr in libmd_mpi_d.a(domdec.o) _lam_mpi_sum$non_lazy_ptr in libmd_mpi_d.a(gmx_wallcycle.o) _lam_mpi_sum$non_lazy_ptr in libmd_mpi_d.a(pme.o) _lam_mpi_comm_world, referenced from: _lam_mpi_comm_world$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_comm_world$non_lazy_ptr in libgmx_mpi_d.a(main.o) _lam_mpi_float, referenced from: _lam_mpi_float$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_double, referenced from: _lam_mpi_double$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(partdec.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(gmx_wallcycle.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(pme.o) _lam_mpi_double$non_lazy_ptr in libmd_mpi_d.a(gmx_parallel_3dfft.o) _lam_mpi_byte, referenced from: _lam_mpi_byte$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(partdec.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(domdec.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(domdec_network.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(pme_pp.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(sim_util.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(pme.o) _lam_mpi_byte$non_lazy_ptr in libmd_mpi_d.a(stat.o) _lam_mpi_int, referenced from: _lam_mpi_int$non_lazy_ptr in libgmx_mpi_d.a(network.o) _lam_mpi_int$non_lazy_ptr in libmd_mpi_d.a(domdec.o) _lam_mpi_int$non_lazy_ptr in libmd_mpi_d.a(pme.o) mpicc tends to be a wrapper script that calls another compiler with the right libraries to compile MPI code for your system. If you had another MPI library installed, then things might get confused. Try mpicc -h or something to get some diagnostic information. You might try to invoke its verbose mode, or to get it to report what libraries it's trying to link. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Question about g_cluster
Jacob Durrant wrote: I recently started using g_cluster and have a question. When I run g_cluster, the program asks me to select two groups. The output looks something like this: Select group for least squares fit and RMSD calculation: Group 0 ( C-alpha) has 383 elements Group 1 ( active_site) has 2438 elements Select a group: 0 Select group for output: Group 0 ( C-alpha) has 383 elements Group 1 ( active_site) has 2438 elements Select a group: 1 I have assumed that g_cluster aligns the trajectory by the first group selected, and then clusters based on the second group. Recently, however, someone told me that both the alignment and the clustering is performed only on the first group. Can anyone confirm this? If so, what's the purpose of the second group? I agree that output is ambiguous. g_cluster -h is also silent on both the need to provide these groups and what they're used for. Perhaps an improvement to the documentation is in order. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] The system setup
Hi I am going to simulate the lysozyme with some ligand in the low ionic strength phosphate buffer . The buffer condition will be (pH 7.2, 8.3 mM) and (pH 5.0 , 8.3 mM) For the buffer condition (pH 7.2, 8.3 mM), I will use TIP3P water model and use CL- ions to nutralize the lysozyme (+8) and cationic ligands. Does my setting make sense? Do you have any suggestion about this ? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] atomic stress distribution map
Hi gmx-users, I am trying to calculate atomic stress distribution on CNT,s but Gromacs gives me just the global stress(virial,Pressure) of the whole system and not the cnt atoms. Could any one suggest me how to calculate atomic site stress for a certain structure in Gromacs? Thanks Farzaneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] The system setup
Chih-Ying Lin wrote: Hi I am going to simulate the lysozyme with some ligand in the low ionic strength phosphate buffer . The buffer condition will be (pH 7.2, 8.3 mM) and (pH 5.0 , 8.3 mM) For the buffer condition (pH 7.2, 8.3 mM), I will use TIP3P water model and use CL- ions to nutralize the lysozyme (+8) and cationic ligands. Does my setting make sense? It makes sense, but it doesn't model those buffer conditions. Calculate how many H+ you'd need in your simulation cell for pH 7.2. Likewise the phosphate species. Do you have any suggestion about this ? Consider the titratable residues when trying to model a system at a different pH. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
