[gmx-users] Has anyone adapted an Allinger force field for GROMACS? (MM,MM+,MM2,MM3...)
Good morning! I would like to use one of the MM force fields (originally by Allinger) in GROMACS. Has anyone tried to adapt such a force field? I know of at least two previous inquiries: Corina Barbu in 2003: http://www.gromacs.org/pipermail/gmx-users/2003-October Konrad Piwowarczyk in 2004: http://www.gromacs.org/pipermail/gmx-users/2004-January/008600.html Thanks in advance, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail.___ 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] Has anyone adapted an Allinger force field for GROMACS? (MM,MM+,MM2,MM3...)
Inon Sharony wrote: Good morning! I would like to use one of the MM force fields (originally by Allinger) in GROMACS. Has anyone tried to adapt such a force field? Short answer: No. It should not be too hard if you want to try (that is if the functional form is implemented already). I know of at least two previous inquiries: Corina Barbu in 2003: http://www.gromacs.org/pipermail/gmx-users/2003-October Konrad Piwowarczyk in 2004: http://www.gromacs.org/pipermail/gmx-users/2004-January/008600.html Thanks in advance, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. ___ 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 -- 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
[gmx-users] Re: MD with RMSD restraint
Hi, Position restraints do not allow me to do what I want. For instance, I want to allow the system to freely explore the conformational space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff. Another application would be to push the system conformation away from the reference structure, by using negative force constants. Therefore the reference structure should be fitted to the simulation structure (or the other way around) before calculating the position differences. Thanks in advance for your help, Sam Mark Abraham wrote: Sam Moors wrote: Hi gmx users/developers, I would like to do a molecular dynamics simulation with a restraint on the backbone RMS deviation from a reference structure. Does anybody know if this is possible? How about position restraints only on the backbone? Same effect. Not exactly as you describe, but you should read the section in chapter 4 of the manual and see for yourself. If yes, could you explain how to do it? If no, what would be the easiest way to implement this in gromacs? It could be done, but I'm not sure it's worth the effort. 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 -- 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 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 77 * ___ 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: MD with RMSD restraint
Sam Moors wrote: Hi, Position restraints do not allow me to do what I want. For instance, I want to allow the system to freely explore the conformational space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff. Another application would be to push the system conformation away from the reference structure, by using negative force constants. Therefore the reference structure should be fitted to the simulation structure (or the other way around) before calculating the position differences. Then you have to derive a force that is the derivative of the RMSD with respect to the positions. This may be difficult, since you have the superposition step in between. What you could do straight away is move from normal RMSD to distance-based RMSD, in which case the this has been implemented using distance restraints. You would use genrestr to generate the additional topology input, then determine a suitable force constant and Bob's your uncle. Cheers. Thanks in advance for your help, Sam Mark Abraham wrote: Sam Moors wrote: Hi gmx users/developers, I would like to do a molecular dynamics simulation with a restraint on the backbone RMS deviation from a reference structure. Does anybody know if this is possible? How about position restraints only on the backbone? Same effect. Not exactly as you describe, but you should read the section in chapter 4 of the manual and see for yourself. If yes, could you explain how to do it? If no, what would be the easiest way to implement this in gromacs? It could be done, but I'm not sure it's worth the effort. 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 -- 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 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 77 * ___ 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 -- 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] Re: MD with RMSD restraint
Another possibility is to patch gromacs with PLUMED http://merlino.mi.infn.it/~plumed/PLUMED/Home.html Here RMSD (and derivatives) is already implemented and you can easily restraint your MD simulation within a certain RMSD cutoff from a reference structure. Massimiliano On May 19, 2009, at 9:31 AM, David van der Spoel wrote: Sam Moors wrote: Hi, Position restraints do not allow me to do what I want. For instance, I want to allow the system to freely explore the conformational space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff. Another application would be to push the system conformation away from the reference structure, by using negative force constants. Therefore the reference structure should be fitted to the simulation structure (or the other way around) before calculating the position differences. Then you have to derive a force that is the derivative of the RMSD with respect to the positions. This may be difficult, since you have the superposition step in between. What you could do straight away is move from normal RMSD to distance-based RMSD, in which case the this has been implemented using distance restraints. You would use genrestr to generate the additional topology input, then determine a suitable force constant and Bob's your uncle. Cheers. Thanks in advance for your help, Sam Mark Abraham wrote: Sam Moors wrote: Hi gmx users/developers, I would like to do a molecular dynamics simulation with a restraint on the backbone RMS deviation from a reference structure. Does anybody know if this is possible? How about position restraints only on the backbone? Same effect. Not exactly as you describe, but you should read the section in chapter 4 of the manual and see for yourself. If yes, could you explain how to do it? If no, what would be the easiest way to implement this in gromacs? It could be done, but I'm not sure it's worth the effort. 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 -- 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 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 77 * ___ 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 -- 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 ___ 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: MD with RMSD restraint
Hi, You can also use essential dynamics sampling. Ran. David van der Spoel wrote: Sam Moors wrote: Hi, Position restraints do not allow me to do what I want. For instance, I want to allow the system to freely explore the conformational space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff. Another application would be to push the system conformation away from the reference structure, by using negative force constants. Therefore the reference structure should be fitted to the simulation structure (or the other way around) before calculating the position differences. Then you have to derive a force that is the derivative of the RMSD with respect to the positions. This may be difficult, since you have the superposition step in between. What you could do straight away is move from normal RMSD to distance-based RMSD, in which case the this has been implemented using distance restraints. You would use genrestr to generate the additional topology input, then determine a suitable force constant and Bob's your uncle. Cheers. Thanks in advance for your help, Sam Mark Abraham wrote: Sam Moors wrote: Hi gmx users/developers, I would like to do a molecular dynamics simulation with a restraint on the backbone RMS deviation from a reference structure. Does anybody know if this is possible? How about position restraints only on the backbone? Same effect. Not exactly as you describe, but you should read the section in chapter 4 of the manual and see for yourself. If yes, could you explain how to do it? If no, what would be the easiest way to implement this in gromacs? It could be done, but I'm not sure it's worth the effort. 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 -- 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 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 77 * ___ 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] .trr forces into VMD
Hi all I am looking for a way to import forces from a gromacs run into VMD for analysis. From a mdrun rerun I have forces in a .trr file but VMD only reads the coordinates. Can you think of any way to get the forces into vmd instead of the coordinates? Thank you! Matteus - Matteus Lindgren, graduate student Department of Chemistry, Umeå University SE-901 87 Umeå, Sweden Phone: +46 (0)90-7865368 ___ 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] Re: MD with RMSD restraint
Hi David, Thanks for your suggestion. However, I have a problem with the use of distance restraints in gromacs. As described in the manual a restraint potential is applied to each pair of atoms separately. Instead, I would like the restraint potential to depend on the root mean square of pair distance deviations, i.e. distance-based RMSD as you suggest. Maybe I can use the averaging over multiple pairs facility, If I change the averaging function (power 2 instead of 6) ? Thanks again, Sam Sam Moors wrote: Hi, Position restraints do not allow me to do what I want. For instance, I want to allow the system to freely explore the conformational space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff. Another application would be to push the system conformation away from the reference structure, by using negative force constants. Therefore the reference structure should be fitted to the simulation structure (or the other way around) before calculating the position differences. Then you have to derive a force that is the derivative of the RMSD with respect to the positions. This may be difficult, since you have the superposition step in between. What you could do straight away is move from normal RMSD to distance-based RMSD, in which case the this has been implemented using distance restraints. You would use genrestr to generate the additional topology input, then determine a suitable force constant and Bob's your uncle. Cheers. Thanks in advance for your help, Sam Mark Abraham wrote: Sam Moors wrote: Hi gmx users/developers, I would like to do a molecular dynamics simulation with a restraint on the backbone RMS deviation from a reference structure. Does anybody know if this is possible? How about position restraints only on the backbone? Same effect. Not exactly as you describe, but you should read the section in chapter 4 of the manual and see for yourself. If yes, could you explain how to do it? If no, what would be the easiest way to implement this in gromacs? It could be done, but I'm not sure it's worth the effort. 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 -- 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 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 77 * ___ 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 -- 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 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 89 * ___ 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: MD with RMSD restraint
Hi, Sorry to pull a self-publicity plug, but you could use our MDDriver library [1] to implement whatever constraint you want as long as it can be calculated from the system positions and translates into forces to be applied to your system. Such a 'scripting' application is very briefly hinted at in the corresponding paper [2]. Cheers, Marc [1] http://www.baaden.ibpc.fr/projects/mddriver/ [2] http://dx.doi.org/10.1002/jcc.21235 David van der Spoel said: Sam Moors wrote: Hi, Position restraints do not allow me to do what I want. For instance, I want to allow the system to freely explore the conformational space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff. Another application would be to push the system conformation away from the reference structure, by using negative force constants. Therefore the reference structure should be fitted to the simulation structure (or the other way around) before calculating the position differences. Then you have to derive a force that is the derivative of the RMSD with respect to the positions. This may be difficult, since you have the superposition step in between. What you could do straight away is move from normal RMSD to distance-based RMSD, in which case the this has been implemented using distance restraints. You would use genrestr to generate the additional topology input, then determine a suitable force constant and Bob's your uncle. Cheers. Thanks in advance for your help, Sam Mark Abraham wrote: Sam Moors wrote: Hi gmx users/developers, I would like to do a molecular dynamics simulation with a restraint on the backbone RMS deviation from a reference structure. Does anybody know if this is possible? How about position restraints only on the backbone? Same effect. Not exactly as you describe, but you should read the section in chapter 4 of the manual and see for yourself. If yes, could you explain how to do it? If no, what would be the easiest way to implement this in gromacs? It could be done, but I'm not sure it's worth the effort. 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 -- 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 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 77 * ___ 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 -- 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 Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 ___ 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.
[gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex
Hello, I have a DNA-Zinc finger complex. What are the suitable forcefields for that type of complexes (the zinc ion is coordinated to 4 deprotonated cysteines)? I need to do some molecular minimization and dynamics including the nucelic acid sequence. Looking for some help. Thank you. Nehme ___ 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] removal of water from hydrophobic core of lipid
Dear all I want remove water molecules from hydrophobic core of lipid by using script Keepbyz.pl by (chris neale) . I want to know basis of deciding uprez and lowrez variables . I mean to say how can I decide which value of uprez and lowrez is suitable for my system protein embedded in lipid bilayer. If anyone did these things please help me in solving this problem. I will be really thankful for that. Nitu Sharma School of Life Sciences Jawaherlal Nehru University New delhi , India ___ 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] removal of water from hydrophobic core of lipid
nitu sharma wrote: Dear all I want remove water molecules from hydrophobic core of lipid by using script Keepbyz.pl by (chris neale) . I want to know basis of deciding uprez and lowrez variables . I mean to say how can I decide which value of uprez and lowrez is suitable for my system protein embedded in lipid bilayer. The bounds of the hydrophobic core (i.e., the start of the acyl chains) are probably a reasonable place to start. -Justin If anyone did these things please help me in solving this problem. I will be really thankful for that. Nitu Sharma School of Life Sciences Jawaherlal Nehru University New delhi , India ___ 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] Hello: Forcefield and potentials for DNA-zinc finger complex
Nehme El Hachem wrote: Hello, I have a DNA-Zinc finger complex. What are the suitable forcefields for that type of complexes (the zinc ion is coordinated to 4 deprotonated cysteines)? The first step is probably to search in the literature for anything similar. Has anyone attempted such work? Is there precedent for making the force field choice? The only force field I know of that contains deprotonated cysteine that has also been implemented in Gromacs is AMBER (residue CYM). The ffamber ports are available for download online. Another thing to consider is whether any MM force field will adequately describe your coordination complex, i.e.: http://wiki.gromacs.org/index.php/Exotic_Species -Justin I need to do some molecular minimization and dynamics including the nucelic acid sequence. Looking for some help. Thank you. Nehme ___ 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 thewww 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] Hello: Forcefield and potentials for DNA-zinc finger complex
Hi, Have a look at http://wiki.gromacs.org/index.php/Parameterization and http://wiki.gromacs.org/index.php/Exotic_Species Next to that, also consider that you are talking about a site with -2 formal charge (ZnS4)2-. How likely is that? From QM studies, it seems much more likely that there are 1 or 2 protons associated with the cluster. If you manage to model that properly, let me know; I'd be interested in that. Cheers, Tsjerk On Tue, May 19, 2009 at 2:01 PM, Nehme El Hachem n...@aub.edu.lb wrote: Hello, I have a DNA-Zinc finger complex. What are the suitable forcefields for that type of complexes (the zinc ion is coordinated to 4 deprotonated cysteines)? I need to do some molecular minimization and dynamics including the nucelic acid sequence. Looking for some help. Thank you. Nehme ___ gmx-users mailing list gmx-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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Selection of force field
Dear all, I want to study glycolipid-protein interaction using united atom GROMACS force field. For lipid simulation we need lipid.itp, which is a mixture of lipid ( Berger) and GROMOS (ffgmxnb) parameters. From an earlier post in gmx-user list, i have come to know that “the ffgmx force field should not be used for production runs. To use popc in simulation, try to dig up popc parameters for a current force field (like ffG43a1)”. Now, as in FF.dat, ffG43a1 is the GROMOS96 force field and ffG43b1, ffG43a2, ffG45a3, ffG53a5 ffG53a6 are the further modifications. For lipid-protein simulation, lots of people are shown to use ffG43a1 parameters. Now, my question is that, if ffG43a1 is better than the other ffG parameters? if not which one should be more appropriate for my glycolipid-protein system (containing sugar moiety)? Looking forward for any reply. thanks in advance, Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/___ 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] .trr forces into VMD
Matteus Lindgren wrote: Hi all I am looking for a way to import forces from a gromacs run into VMD for analysis. From a mdrun –rerun I have forces in a .trr file but VMD only reads the coordinates. Can you think of any way to get the forces into vmd instead of the coordinates? If VMD will only import positions from .trr files, then you could write a forces-only .trr file and through a code hack or hex edit, force the frame header to describe them as positions. Or, write a new VMD plugin. Or, modify the VMD source suitably. 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] Test suit failures
Dear gmx-users, I have done a test using test suit 4.0.4, and I got some failures as follows. All 16 simple tests PASSED FAILED. Check files in aminoacids FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in water 4 out of 14 complex tests FAILED FAILED. Check files in kernel020 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 16 out of 63 kernel tests FAILED All 45 pdb2gmx tests PASSED My gcc version is 4.1.1, and both gmx 4.0.4 and 4.0.5 get exactly the same failures on my Xeon 8 core based linux. For example, in /kernel/kernel020 checkpot.out gives: -- comparing energy file reference_s.edr and ener.edr There are 39 terms in the energy files There are 12 terms to compare in the energy files LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 Files read succesfully -- checkvir.out gives: -- comparing energy file reference_s.edr and ener.edr There are 39 terms in the energy files There are 25 terms to compare in the energy files LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 Kinetic En. step 0: 15.0135, step 0: 29.0739 Total Energy step 0: -306.588, step 0: -222.898 Temperature step 0: 1.93226, step 0: 3.74185 Pressure (bar) step 0: -3095.37, step 0: -2497.79 Vir-XX step 0: 1127.45, step 0: 1075.85 Vir-XY step 0:63.524, step 0: 21.7761 Vir-XZ step 0: -264.813, step 0: -260.354 Vir-YX step 0: 63.5241, step 0: 21.777 Vir-YY step 0: 803.252, step 0: 581.702 Vir-ZX step 0: -264.813, step 0: -260.354 Vir-ZZ step 0: 321.207, step 0: 176.573 Files read succesfully The deviations are obvious. Any suggestion would be appreciate. Thank you. Best Regards, Bert ___ 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] Test suit failures
Bert wrote: Dear gmx-users, I have done a test using test suit 4.0.4, and I got some failures as follows. All 16 simple tests PASSED FAILED. Check files in aminoacids FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in water 4 out of 14 complex tests FAILED Check the files in these directories to see if the differences are acceptable, as explained on the wiki: http://wiki.gromacs.org/index.php/Test-Set snip 16 out of 63 kernel tests FAILED These failures are a known issue and a bugzilla has been filed. They affect Buckingham interactions. All 45 pdb2gmx tests PASSED My gcc version is 4.1.1, and both gmx 4.0.4 and 4.0.5 get exactly the same failures on my Xeon 8 core based linux. For example, in /kernel/kernel020 As warned on the Gromacs site: WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc. Users have reported non-functional or improperly-functioning executables produced by the 4.1.x series. -Justin checkpot.out gives: -- comparing energy file reference_s.edr and ener.edr There are 39 terms in the energy files There are 12 terms to compare in the energy files LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 Files read succesfully -- checkvir.out gives: -- comparing energy file reference_s.edr and ener.edr There are 39 terms in the energy files There are 25 terms to compare in the energy files LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 Kinetic En. step 0: 15.0135, step 0: 29.0739 Total Energy step 0: -306.588, step 0: -222.898 Temperature step 0: 1.93226, step 0: 3.74185 Pressure (bar) step 0: -3095.37, step 0: -2497.79 Vir-XX step 0: 1127.45, step 0: 1075.85 Vir-XY step 0:63.524, step 0: 21.7761 Vir-XZ step 0: -264.813, step 0: -260.354 Vir-YX step 0: 63.5241, step 0: 21.777 Vir-YY step 0: 803.252, step 0: 581.702 Vir-ZX step 0: -264.813, step 0: -260.354 Vir-ZZ step 0: 321.207, step 0: 176.573 Files read succesfully The deviations are obvious. Any suggestion would be appreciate. Thank you. Best Regards, Bert ___ 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] .trr forces into VMD
Hi, g_traj can write |f| or components of f in the b-factor field of a pdb file. I guess VMD can read and display that. I don't know if that will fulfill your needs. Berk Date: Wed, 20 May 2009 00:19:59 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] .trr forces into VMD Matteus Lindgren wrote: Hi all I am looking for a way to import forces from a gromacs run into VMD for analysis. From a mdrun –rerun I have forces in a .trr file but VMD only reads the coordinates. Can you think of any way to get the forces into vmd instead of the coordinates? If VMD will only import positions from .trr files, then you could write a forces-only .trr file and through a code hack or hex edit, force the frame header to describe them as positions. Or, write a new VMD plugin. Or, modify the VMD source suitably. 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 _ 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
[gmx-users] how to apply shear force
Hi all users, I am wondering how I can apply the shear force into the gromacs .Does anyone has such experoence about that? Really appreciate any suggestions. Yang ___ 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] how to apply shear force
Hi, Read the pdf manual, it has an index entry for shear. Berk From: yang...@mavs.uta.edu To: gmx-users@gromacs.org Date: Tue, 19 May 2009 15:10:24 + Subject: [gmx-users] how to apply shear force Hi all users, I am wondering how I can apply the shear force into the gromacs .Does anyone has such experoence about that? Really appreciate any suggestions. Yang ___ 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
[gmx-users] FudgeQQ parameter with TraPPE FF and OPLS-AA
Dear GMX-users. I'm trying to do free energy calculations for calculations of partitions coefficients. My normal defaults section of TraPPE topologies are: ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 no 0.5 0.5 because TraPPE don't use 1-4 LJ interaction, and I have read that FudgeQQ always apply even though gen-pairs=no. Now I want to do my calculations with OPLS-AA for the solute molecule, and TraPPE-UA for the solvent, so my default section must now be: ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.5 , but the problem arises when I have for instance Ethanol in my solvent, then gen-pair will calculate LJ 1-4 interactions for the Ethanol as well. But if I in the .top for the ethanol pair write: [ pairs ] ; ai aj funct c6 c12 1 4 1 0.00e+00 0.00e+00; then will the 1-4 LJ be 0, but the 1-4 Coulomb will still be calculated - right?? Also, can I check all the interaction parameters calculated and inserted by grompp? Best regards. Rasmus Lundsgaard ___ 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] How can i know if the protein swell during the MD simulation?
sovent accesible surface area? On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: stretching != swelling, e.g. On Mon, May 18, 2009 at 10:46 AM, Bhanu bhanui...@gmail.com wrote: How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of the protein is still a matter of setting your criteria and finding the right tools to assess these. Not the simplest thing... Cheers, Tsjerk On Mon, May 18, 2009 at 12:22 AM, Justin A. Lemkul jalem...@vt.edu wrote: Chih-Ying Lin wrote: HI How can i know if the protein swell during the MD simulation? What are those indications to see the swollen protein? How do you define the term swelling? This again sounds like another issue on defining your own criteria for the expected behavior and reading the manual about available analysis tools. -Justin 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 -- 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] gromacs on glacier.westgrid.ca
Hi All, Is there anyone who is running gromacs on glacier.westgrid.ca machine? If yes, I will be appreciated if he/she can tell me how to run gmx on this facility. I either get error messages which says either the executable or the topology file can not be found. Regards, Payman ___ 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] How can i know if the protein swell during the MD simulation?
Well, why didn't I think of that? Maybe because flattening will also increase the SAS, or (partial) unfolding, or opening of two domains... :) Tsjerk On Tue, May 19, 2009 at 6:10 PM, Marius Retegan marius.s.rete...@gmail.com wrote: sovent accesible surface area? On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: stretching != swelling, e.g. On Mon, May 18, 2009 at 10:46 AM, Bhanu bhanui...@gmail.com wrote: How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of the protein is still a matter of setting your criteria and finding the right tools to assess these. Not the simplest thing... Cheers, Tsjerk On Mon, May 18, 2009 at 12:22 AM, Justin A. Lemkul jalem...@vt.edu wrote: Chih-Ying Lin wrote: HI How can i know if the protein swell during the MD simulation? What are those indications to see the swollen protein? How do you define the term swelling? This again sounds like another issue on defining your own criteria for the expected behavior and reading the manual about available analysis tools. -Justin Thank you Lin ___ gmx-users mailing list gmx-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 -- 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 list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-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 -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-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 ___ gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar,
Re: [gmx-users] shift function for vdwtype and density
Dear David: Thank you so much for the valuable information. Our conclusion in the above paper is to use PME for Coulomb and not shift Van der Waals I have read the paper you mentioned and did not find how you treated the VdW. Have you done some work on the cut off method for vdw? Since I used PME for Coulomb in my system. I am still confusing why not shift for vdw. I would also recommend to use TIP4P rather than TIP5P, as Jorgensen uses TIP4P for all his parameterizations. I have read Jorgensen's paper for the OPLS and realized that the TIP4P would be the first choice for combining with OPLS. However my concern is that TIP4P model is not as good as TIP5P in terms of diffusion constant and viscosity which are extremely important for my purpose. I also have compared SPC and TIP4P and turn out that SPC can give a better result for my system. Unfornately SPC has a very bad viscosity as TIP4P. So I am trying TIP5P. Do you think OPLS+ TIP5P can cause serious problem or horrible artifacts. If you can suggest some literatures on this that would be great. I really appericate all your help! On Mon, May 18, 2009 at 10:37 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: Justin A. Lemkul wrote: Yanmei Song wrote: Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if it result in larger density? Thank you so much! No. My suggestion is to do your homework, as Mark originally said, and as I echoed in my last mail. Read about the water model, its expected performance under different simulation parameters, and evaluate what you want to do once you have done this background work. If you have done a thorough literature review, there is no one else that can make a choice for you; decide how to handle your system based on what you read. Actually this is not so easy. Jorgensen has never published the way he treats cut-offs, but he was friendly enough to let me know, so we have actually done it: David van der Spoel and Paul J. van Maaren: The origin of layer structure artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11 (2006) If you look in the appendix you can find the one and only OPLS. However This is not to be recommended since the effect is very different for MD and MC (what Jorgensen uses). In MD the official method will give horrible artifacts. In other words, you have to use something better. Our conclusion in the above paper is to use PME for Coulomb and not shift Van der Waals. I would also recommend to use TIP4P rather than TIP5P, as Jorgensen uses TIP4P for all his parameterizations. -Justin On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get? Every parameter you specify will affect the results you see. I agree with Mark - look up the original reference for TIP5P and see what parameters are recommended. Also read the subsequent literature that has used TIP5P to see what modifications (electrostatic treatment, vdW treatment, etc) are appropriate or even more accurate. Also realize that using vdwtype = shift may not be the best solution. I only suggested as a guess for something to try back when you were getting bizarre results with your polymer. Have you ever tried dispersion correction when using vdwtype = cutoff? I routinely use such a setup and have never seen any really bizarre behavior. -Justin On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! So your system is water + polymer? In that case, you have an added variable - the
Re: [gmx-users] Re: MD with RMSD restraint
Sam Moors wrote: Hi David, Thanks for your suggestion. However, I have a problem with the use of distance restraints in gromacs. As described in the manual a restraint potential is applied to each pair of atoms separately. Instead, I would like the restraint potential to depend on the root mean square of pair distance deviations, i.e. distance-based RMSD as you suggest. Maybe I can use the averaging over multiple pairs facility, If I change the averaging function (power 2 instead of 6) ? If the averaging is purely harmonic there is no difference. For this, turn off r^-3 averaging etc. in the mdp file. Thanks again, Sam Sam Moors wrote: Hi, Position restraints do not allow me to do what I want. For instance, I want to allow the system to freely explore the conformational space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff. Another application would be to push the system conformation away from the reference structure, by using negative force constants. Therefore the reference structure should be fitted to the simulation structure (or the other way around) before calculating the position differences. Then you have to derive a force that is the derivative of the RMSD with respect to the positions. This may be difficult, since you have the superposition step in between. What you could do straight away is move from normal RMSD to distance-based RMSD, in which case the this has been implemented using distance restraints. You would use genrestr to generate the additional topology input, then determine a suitable force constant and Bob's your uncle. Cheers. Thanks in advance for your help, Sam Mark Abraham wrote: Sam Moors wrote: Hi gmx users/developers, I would like to do a molecular dynamics simulation with a restraint on the backbone RMS deviation from a reference structure. Does anybody know if this is possible? How about position restraints only on the backbone? Same effect. Not exactly as you describe, but you should read the section in chapter 4 of the manual and see for yourself. If yes, could you explain how to do it? If no, what would be the easiest way to implement this in gromacs? It could be done, but I'm not sure it's worth the effort. 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 -- 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 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 77 * ___ 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 -- 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 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 89 * ___ 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 -- 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
Re: [gmx-users] gromacs on glacier.westgrid.ca
Hi Payman, That is probably not the only grid facility on which Gromacs may be run and it would be helpful if you could give specifications of it (WMS software e.g.), which could give you more response. Also, it would be helpful if you'd be able to give more information regarding the output. Then you'd also have to ask the question whether your problem is grid related or gromacs related. In the former case you'd better consult support from the facility you're trying to use. Cheers, Tsjerk On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh ppirz...@ucalgary.ca wrote: Hi All, Is there anyone who is running gromacs on glacier.westgrid.ca machine? If yes, I will be appreciated if he/she can tell me how to run gmx on this facility. I either get error messages which says either the executable or the topology file can not be found. Regards, Payman ___ gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] gromacs on glacier.westgrid.ca
Dear Tsjerk, Thanks for your e-mail. The message that cluster sends is: Running on 4 processors. Starting run at: Sat May 16 17:13:28 PDT 2009 Warning: Command line arguments for program should be given after the program name. Assuming that ./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that -s is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that npttest is a command line argument for the program. Missing: program name Program -path either does not exist, is not executable, or is an erroneous argument to mpirun. Job finished at: Sat May 16 17:13:28 PDT 2009 The message that GROMACS has in log file is: Program mdrun, VERSION 3.3.1 Source code file: gmxfio.c, line: 706 Can not open file: topol.tpr This is while I have the topology file in the same folder. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar Sent: May 19, 2009 12:25 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca Hi Payman, That is probably not the only grid facility on which Gromacs may be run and it would be helpful if you could give specifications of it (WMS software e.g.), which could give you more response. Also, it would be helpful if you'd be able to give more information regarding the output. Then you'd also have to ask the question whether your problem is grid related or gromacs related. In the former case you'd better consult support from the facility you're trying to use. Cheers, Tsjerk On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh ppirz...@ucalgary.ca wrote: Hi All, Is there anyone who is running gromacs on glacier.westgrid.ca machine? If yes, I will be appreciated if he/she can tell me how to run gmx on this facility. I either get error messages which says either the executable or the topology file can not be found. Regards, Payman ___ gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] gromacs on glacier.westgrid.ca
Payman Pirzadeh wrote: Dear Tsjerk, Thanks for your e-mail. The message that cluster sends is: Running on 4 processors. Starting run at: Sat May 16 17:13:28 PDT 2009 Warning: Command line arguments for program should be given after the program name. Assuming that ./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that -s is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that npttest is a command line argument for the program. Missing: program name Program -path either does not exist, is not executable, or is an erroneous argument to mpirun. Job finished at: Sat May 16 17:13:28 PDT 2009 The message that GROMACS has in log file is: Program mdrun, VERSION 3.3.1 Source code file: gmxfio.c, line: 706 Can not open file: topol.tpr This is while I have the topology file in the same folder. It might be useful to post the script you're using to submit the job. There's something (or several things) fundamentally wrong. Your path points to Gromacs version 4.0.4, but the executable that's being called is version 3.3.1. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar Sent: May 19, 2009 12:25 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca Hi Payman, That is probably not the only grid facility on which Gromacs may be run and it would be helpful if you could give specifications of it (WMS software e.g.), which could give you more response. Also, it would be helpful if you'd be able to give more information regarding the output. Then you'd also have to ask the question whether your problem is grid related or gromacs related. In the former case you'd better consult support from the facility you're trying to use. Cheers, Tsjerk On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh ppirz...@ucalgary.ca wrote: Hi All, Is there anyone who is running gromacs on glacier.westgrid.ca machine? If yes, I will be appreciated if he/she can tell me how to run gmx on this facility. I either get error messages which says either the executable or the topology file can not be found. Regards, Payman ___ 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] shift function for vdwtype and density
Dear all: This is the mdp I just used for the system. The funny thing is after a 8ns simulation I got a very high pressure and temperature: Temperature 343.437 Pressure (bar) 45.782 I also did another run with removing the vdw_switch in mdp and keep all other condition unchanged. I got good result. The following is my mdp: cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 2000 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = Shift rvdw_switch = 0.8 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.0 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = PDM ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 On Tue, May 19, 2009 at 11:12 AM, Yanmei Song yson...@asu.edu wrote: Dear David: Thank you so much for the valuable information. Our conclusion in the above paper is to use PME for Coulomb and not shift Van der Waals I have read the paper you mentioned and did not find how you treated the VdW. Have you done some work on the cut off method for vdw? Since I used PME for Coulomb in my system. I am still confusing why not shift for vdw. I would also recommend to use TIP4P rather than TIP5P, as Jorgensen uses TIP4P for all his parameterizations. I have read Jorgensen's paper for the OPLS and realized that the TIP4P would be the first choice for combining with OPLS. However my concern is that TIP4P model is not as good as TIP5P in terms of diffusion constant and viscosity which are extremely important for my purpose. I also have compared SPC and TIP4P and turn out that SPC can give a better result for my system. Unfornately SPC has a very bad viscosity as TIP4P. So I am trying TIP5P. Do you think OPLS+ TIP5P can cause serious problem or horrible artifacts. If you can suggest some literatures on this that would be great. I really appericate all your help! On Mon, May 18, 2009 at 10:37 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Justin A. Lemkul wrote: Yanmei Song wrote: Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if it result in larger density? Thank you so much! No. My suggestion is to do your homework, as Mark originally said, and as I echoed in my last mail. Read about the water model, its expected performance under different simulation parameters, and evaluate what you want to do once you have done this background work. If you have done a thorough literature review, there is no one else that can make a choice for you; decide how to handle your system based on what you read. Actually this is not so easy. Jorgensen has never published the way he treats cut-offs, but he was friendly enough to let me know, so we have actually done it: David van der Spoel and Paul J. van Maaren: The origin of layer structure artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11 (2006) If you look in the appendix you can find the one and only OPLS. However This is not to be recommended since the effect is very different for MD and MC (what Jorgensen uses). In MD the official method will give horrible artifacts. In other words, you have to use something better. Our conclusion in the above paper is to use PME for Coulomb and not shift Van der Waals. I would also recommend to use TIP4P rather than TIP5P, as Jorgensen uses TIP4P for all his parameterizations. -Justin On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger
RE: [gmx-users] gromacs on glacier.westgrid.ca
Hi Justin,
Following is the script I use. But remember several points:
1. I compiled the gmx with double precision and did not rename the code to
mpi. I kept whatever was produced with _d suffix.
2. I use the same script for other codes and they work (I am using other MD
code for special purposes and a QM code as well).
3. This script follows the guidelines of glacier as well. It is available
online at http://www.westgrid.ca/support/quickstart/glacier
#!/bin/bash
#PBS -S /bin/bash
# Torque script for running an MPI program pn on glacier
# 2005-05-26 DSP
# This presumes code compiled with the Intel compiler.
# For example:
# /global/software/mpich-1.2.5.2/ssh/bin/mpif90 pn.f -o pn
#PBS -N sixsite-test
#PBS -l walltime=240:00:00
#PBS -l nodes=2:ppn=2
#PBS -l qos=parallel
MPIRUN=/global/software/mpich-1.2.5.2/ssh/bin/mpirun
cd $PBS_O_WORKDIR
echo Current working directory is `pwd`
echo Node file: $PBS_NODEFILE :
echo -
cat $PBS_NODEFILE
echo -
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo Running on $NUM_PROCS processors.
echo Starting run at: `date`
${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest
echo Job finished at: `date`
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: May 19, 2009 12:36 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] gromacs on glacier.westgrid.ca
Dear Tsjerk,
Thanks for your e-mail. The message that cluster sends is:
Running on 4 processors.
Starting run at: Sat May 16 17:13:28 PDT 2009
Warning: Command line arguments for program should be given
after the program name. Assuming that
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that -s is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that npttest is a
command line argument for the program.
Missing: program name
Program -path either does not exist, is not
executable, or is an erroneous argument to mpirun.
Job finished at: Sat May 16 17:13:28 PDT 2009
The message that GROMACS has in log file is:
Program mdrun, VERSION 3.3.1
Source code file: gmxfio.c, line: 706
Can not open file:
topol.tpr
This is while I have the topology file in the same folder.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Tsjerk Wassenaar
Sent: May 19, 2009 12:25 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca
Hi Payman,
That is probably not the only grid facility on which Gromacs may be
run and it would be helpful if you could give specifications of it
(WMS software e.g.), which could give you more response. Also, it
would be helpful if you'd be able to give more information regarding
the output. Then you'd also have to ask the question whether your
problem is grid related or gromacs related. In the former case you'd
better consult support from the facility you're trying to use.
Cheers,
Tsjerk
On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh ppirz...@ucalgary.ca
wrote:
Hi All,
Is there anyone who is running gromacs on glacier.westgrid.ca machine? If
yes, I will be appreciated if he/she can tell me how to run gmx on this
facility. I either get error messages which says either the executable or
the topology file can not be found.
Regards,
Payman
___
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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Re: [gmx-users] gromacs on glacier.westgrid.ca
Payman Pirzadeh wrote:
Hi Justin,
Following is the script I use. But remember several points:
1. I compiled the gmx with double precision and did not rename the code to
mpi. I kept whatever was produced with _d suffix.
Whatever was produced does not inspire confidence. You're sure that
--enable-mpi was used during configuration, right?
2. I use the same script for other codes and they work (I am using other MD
code for special purposes and a QM code as well).
There has to be something different about this one. If everything worked, we
wouldn't be having this conversation :)
3. This script follows the guidelines of glacier as well. It is available
online at http://www.westgrid.ca/support/quickstart/glacier
#!/bin/bash
#PBS -S /bin/bash
# Torque script for running an MPI program pn on glacier
# 2005-05-26 DSP
# This presumes code compiled with the Intel compiler.
# For example:
# /global/software/mpich-1.2.5.2/ssh/bin/mpif90 pn.f -o pn
#PBS -N sixsite-test
#PBS -l walltime=240:00:00
#PBS -l nodes=2:ppn=2
#PBS -l qos=parallel
MPIRUN=/global/software/mpich-1.2.5.2/ssh/bin/mpirun
cd $PBS_O_WORKDIR
echo Current working directory is `pwd`
echo Node file: $PBS_NODEFILE :
echo -
cat $PBS_NODEFILE
echo -
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo Running on $NUM_PROCS processors.
echo Starting run at: `date`
${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest
echo Job finished at: `date`
Based on the error messages, it appears that mpirun is interpreting everything
you have specified as a command line argument (the call to mdrun_d, -deffnm,
npttest). We have the same version of mpirun on our cluster, and -path does not
appear to be a valid argument. Perhaps try something like:
MDRUN=/global/home/prizadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest
${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE ${MDRUN}
-Justin
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: May 19, 2009 12:36 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] gromacs on glacier.westgrid.ca
Dear Tsjerk,
Thanks for your e-mail. The message that cluster sends is:
Running on 4 processors.
Starting run at: Sat May 16 17:13:28 PDT 2009
Warning: Command line arguments for program should be given
after the program name. Assuming that
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that -s is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that npttest is a
command line argument for the program.
Missing: program name
Program -path either does not exist, is not
executable, or is an erroneous argument to mpirun.
Job finished at: Sat May 16 17:13:28 PDT 2009
The message that GROMACS has in log file is:
Program mdrun, VERSION 3.3.1
Source code file: gmxfio.c, line: 706
Can not open file:
topol.tpr
This is while I have the topology file in the same folder.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Tsjerk Wassenaar
Sent: May 19, 2009 12:25 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca
Hi Payman,
That is probably not the only grid facility on which Gromacs may be
run and it would be helpful if you could give specifications of it
(WMS software e.g.), which could give you more response. Also, it
would be helpful if you'd be able to give more information regarding
the output. Then you'd also have to ask the question whether your
problem is grid related or gromacs related. In the former case you'd
better consult support from the facility you're trying to use.
Cheers,
Tsjerk
On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh ppirz...@ucalgary.ca
wrote:
Hi All,
Is there anyone who is running gromacs on glacier.westgrid.ca machine? If
yes, I will be appreciated if he/she can tell me how to run gmx on this
facility. I either get error messages which says either the executable or
the topology file can not be found.
Regards,
Payman
___
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 |
[gmx-users] dt = 0.002
Hi I want to get the simulation results fater and want to set the time step dt = 0.002 what is the upper limit of the time step dt ? 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
Re: [gmx-users] dt = 0.002
Chih-Ying Lin wrote: Hi I want to get the simulation results fater and want to set the time step dt = 0.002 what is the upper limit of the time step dt ? Some textbook reading is probably in order here. Also of interest are papers describing constraint algorithms. Ultimately the timestep will be dependent upon energy conservation, choice of virtual sites, etc. The manual will also provide some relevant information. -Justin 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 -- 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] dt = 0.002
Hi Lin, I would suggest taking a look at the manual, specifically section 6.5 (Removing Fastest Degrees of Freedom), and any general textbook on molecular simulation. Wanting faster results without having an understanding of the method is a good recipe for getting the wrong answer. There are physical and numerical reasons for the parameter choices and it would be good to understand those before proceeding further with molecular dynamics. Best of luck, Josh On May 19, 2009, at 2:27 PM, Chih-Ying Lin wrote: Hi I want to get the simulation results fater and want to set the time step dt = 0.002 what is the upper limit of the time step dt ? 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 -- Joshua L. Adelman Biophysics Graduate Group Lab: 510.643.2159 218 Wellman HallFax: 510.642.7428 University of California, Berkeley http://nature.berkeley.edu/ ~jadelman Berkeley, CA 94720 USA jadel...@berkeley.edu -- ___ 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] g_clustsize method
I am planning on using g_clustsize to do some condensation analysis. I looked at g_cluster and see that it has a number of method options including single linkage and jarvis patrick. Is it true that g_clustsize has only the single linkage option? I took a look at the source code but this type of thing is not my strength. ___ 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] shift function for vdwtype and density
Yanmei Song wrote: Dear all: This is the mdp I just used for the system. The funny thing is after a 8ns simulation I got a very high pressure and temperature: Temperature 343.437 Pressure (bar) 45.782 I also did another run with removing the vdw_switch in mdp and keep all other condition unchanged. I got good result. The following is my mdp: cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! I'd suspect that this value for dt is also not likely to have been used during parameterization. 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] mdp file for local pressure
Is there a local pressure version of Gromacs 4? I can only find Gromacs version 3.02 with local pressure. If there is, could you tell me where to get it? Thanks. Daniel From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of anirban polley Sent: Monday, May 18, 2009 7:39 PM To: gmx-users@gromacs.org Subject: [gmx-users] mdp file for local pressure --- Program grompp_mpi, VERSION 4.0.2_localpressure Source code file: readir.c, line: 454 Fatal error: Expected 2 elements for wall_atomtype, found 0 --- Could you please tell me where my fault is? Thanks a lot in advance. Anirban This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. ___ 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] g_clustsize method
Jacob Spooner wrote: I am planning on using g_clustsize to do some condensation analysis. I looked at g_cluster and see that it has a number of method options including single linkage and jarvis patrick. Is it true that g_clustsize has only the single linkage option? I took a look at the source code but this type of thing is not my strength. ___ 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 Yes. Is that not sufficient? -- 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
