Re: [gmx-users] anisotropic pressure coupling for temperature annealing
Have you simulated the system without the annealing, to see if it does the same thing? Bilayers are very sensitive to minor changes in setup, using someone else's equilibrated bilayer coordinates doesn't mean it's equilibrated for your system. - Original Message From: Q733 [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, October 10, 2007 6:40:06 AM Subject: [gmx-users] anisotropic pressure coupling for temperature annealing Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x dimension and y dimension increased with time in the whole procedure, but actually the area/lipid should decrease when tempreture decreases. I think there may due to the P couple parameters I used. Now I write them here: tau_p = 2.0 2.0 2.0 0 0 0 compressibility = 4.5e-6 4.5e-6 4.5e-6 0 0 0 ref_p = 11 1 1 1 1 Is there anything wrong with my parameter? or should I use ref_p = 11 1 0 0 0 I saw someone use this ref_p before. Any suggestion will be appreciated, thanks in advance. Catch up on fall's hot new shows on Yahoo! TV. Watch previews, get listings, and more! http://tv.yahoo.com/collections/3658 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to change the box size during simuation
You can apply external forces to subsets of atoms, in such a way as to cause your box to shrink by itself. - Original Message From: WU Yanbin [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Tuesday, October 9, 2007 11:40:21 PM Subject: [gmx-users] How to change the box size during simuation Hey, Now I'm simulating infinite molecules. I want to change the box size a lit bit every time step so as to induce some stress in this system. Is there any way in gromacs to do this, apart from modifying the code? Thanks in advance. Yours Sincerely, WU Yanbin Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] How to change the box size during simuation
From: WU Yanbin [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] How to change the box size during simuation Date: Tue, 9 Oct 2007 17:40:21 -0500 Hey, Now I'm simulating infinite molecules. I want to change the box size a lit bit every time step so as to induce some stress in this system. Is there any way in gromacs to do this, apart from modifying the code? You can use pressure coupling to apply a stress and induce a strain or you can use the deform option to apply a strain and induce stress. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] What is this warning on running grompp ? WARNING 1 [file md-new.mdp, line unknown]
Hi, When running grompp I get the following error often ### checking input for internal consistency... WARNING 1 [file md-new.mdp, line unknown]: ### It does not look like a critical error, but I want to make sure. Did not find any specific discussions on the mailing list immediately. My md-new.mdp file is attached. Thank you for the help. Also, how can one send a reply to a specific message in the list ? Thanks very much ! -Maria -- Maria G. Technical University of Denmark Copenhagen md-new.mdp Description: application/mdp ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] xtc error
Hi All, I had this problem running MD on a single Debian machine: Program mdrun_d, VERSION 3.3.1 Source code file: stat.c, line: 257 Fatal error: XTC error There is no chance of being size exceeded of file or quota, or disk error. I compiled gromacs with gcc-3.4... Does anyone know what this error means? Gcc version may be the cause? Thanks, Luciano P Gomes ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] xtc error
luciano.pgomes wrote: Hi All, I had this problem running MD on a single Debian machine: Program mdrun_d, VERSION 3.3.1 Source code file: stat.c, line: 257 Fatal error: XTC error it can also mean that your system is exploding. There is no chance of being size exceeded of file or quota, or disk error. I compiled gromacs with gcc-3.4... Does anyone know what this error means? Gcc version may be the cause? Thanks, Luciano P Gomes ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Criteria and Energy Conservation
[EMAIL PROTECTED] wrote: Dear GROMACS Users, I'm trying to use GROMACS to get some MD snapshots for single-point quantum mechanical calculations, trying to observe HOMO-LUMO gap of a protein immersed in water with counterions, at a given salt concentration (4600 atoms in total). I'd like to know if they are reliable enough to send to QM calculations. I've got two questions: Which are the criteria I should be looking at? And one of them I've analyzed was energy conservation (I'm doing 300K NVT MD, with 10A cutoff for vdw and coulomb, with PME electrostatics, and double precision), and the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but I've got 0.3-0.5 in all simulations I've done. What should I do? This is because of T coupling. If you turn off T coupling it will be better (but you will not have constant T, and the energy will dirft in the long run). Your starting structures are fine for QM, but QM minimization will take a LONG time. Thanks in advance, Gustavo Troiano Feliciano This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulating hydrocarbons in water
Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I've built topologies for hexadecane compatible with NAMD, so I figure I should be able to do the same in Gromacs but I'm fuzzy on how to go about doing so (what files to edit). I was also hoping to get some input on which forcefield would be best for this sort of system. I'd greatly appreciate it if someone could give me some pointers on how to get started here. Thanks very much, Adam ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulating hydrocarbons in water
Adam Fraser wrote: Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I've built topologies for hexadecane compatible with NAMD, so I figure I should be able to do the same in Gromacs but I'm fuzzy on how to go about doing so (what files to edit). I was also hoping to get some input on which forcefield would be best for this sort of system. I'd greatly appreciate it if someone could give me some pointers on how to get started here. Thanks very much, Adam if you have a pdb file you can run x2top (3.3.2 only). ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulating hydrocarbons in water
Yes I tried this and it doesn't work for me. I get: Fatal error: Library file ffG53a6.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script that converts pdb to gro, and I still get the above error. -Adam On 10/10/07, David van der Spoel [EMAIL PROTECTED] wrote: Adam Fraser wrote: Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I've built topologies for hexadecane compatible with NAMD, so I figure I should be able to do the same in Gromacs but I'm fuzzy on how to go about doing so (what files to edit). I was also hoping to get some input on which forcefield would be best for this sort of system. I'd greatly appreciate it if someone could give me some pointers on how to get started here. Thanks very much, Adam if you have a pdb file you can run x2top (3.3.2 only). ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulating hydrocarbons in water
Just as a note editconf will covert a pdb to a gro file Tom --On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser [EMAIL PROTECTED] wrote: Yes I tried this and it doesn't work for me. I get: Fatal error: Library file ffG53a6.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script that converts pdb to gro, and I still get the above error. -Adam On 10/10/07, David van der Spoel [EMAIL PROTECTED] wrote: Adam Fraser wrote: Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I've built topologies for hexadecane compatible with NAMD, so I figure I should be able to do the same in Gromacs but I'm fuzzy on how to go about doing so (what files to edit). I was also hoping to get some input on which forcefield would be best for this sort of system. I'd greatly appreciate it if someone could give me some pointers on how to get started here. Thanks very much, Adam if you have a pdb file you can run x2top (3.3.2 only). ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Criteria and Energy Conservation
Thank you very much again, David! Then it's fine for me, since what I want to do is a single point QM in termalized snapshots of the dynamics and not QM minimization. Gustavo [EMAIL PROTECTED] wrote: Dear GROMACS Users, I'm trying to use GROMACS to get some MD snapshots for single-point quantum mechanical calculations, trying to observe HOMO-LUMO gap of a protein immersed in water with counterions, at a given salt concentration (4600 atoms in total). I'd like to know if they are reliable enough to send to QM calculations. I've got two questions: Which are the criteria I should be looking at? And one of them I've analyzed was energy conservation (I'm doing 300K NVT MD, with 10A cutoff for vdw and coulomb, with PME electrostatics, and double precision), and the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but I've got 0.3-0.5 in all simulations I've done. What should I do? This is because of T coupling. If you turn off T coupling it will be better (but you will not have constant T, and the energy will dirft in the long run). Your starting structures are fine for QM, but QM minimization will take a LONG time. Thanks in advance, Gustavo Troiano Feliciano This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulating hydrocarbons in water
Adam Fraser wrote: Yes I tried this and it doesn't work for me. I get: Fatal error: Library file ffG53a6.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) did you use 3.3.2 ? The default and only supported FF there is OPLS. For GROMOS variants you can try the prodrg webserver. Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script that converts pdb to gro, and I still get the above error. -Adam On 10/10/07, * David van der Spoel* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Adam Fraser wrote: Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I've built topologies for hexadecane compatible with NAMD, so I figure I should be able to do the same in Gromacs but I'm fuzzy on how to go about doing so (what files to edit). I was also hoping to get some input on which forcefield would be best for this sort of system. I'd greatly appreciate it if someone could give me some pointers on how to get started here. Thanks very much, Adam if you have a pdb file you can run x2top (3.3.2 only). ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] mailto:[EMAIL PROTECTED][EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] xtc error
Hi, Hi All, I had this problem running MD on a single Debian machine: Program mdrun_d, VERSION 3.3.1 Source code file: stat.c, line: 257 Fatal error: XTC error There is no chance of being size exceeded of file or quota, or disk error. I compiled gromacs with gcc-3.4... Does anyone know what this error means? Gcc version may be the cause? Thanks, Luciano P Gomes it can also mean that your system is exploding. No. The xtc file doesn't opened. It crashed VMD. I forgot saying that I was running simulated annealing protocol with a DNA molecule and crystallographic water molecules (HOH) freezed, only moving ions and water molecules placed by genbox (tip3p). The crash occured on 2 ps of simulation time in a temperature of 50K. I had excluded non-bonded interactions: DNA DNA HOH DNA HOH HOH. I am running now a simple MD at 300K and this error haven't occured yet. I am trying to understand... Thanks, Luciano ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Criteria and Energy Conservation
[EMAIL PROTECTED] wrote: Thank you very much again, David! Then it's fine for me, since what I want to do is a single point QM in termalized snapshots of the dynamics and not QM minimization. But then you will get systematically incorrect energies due to weird (force field dependent) bond lengths etc. Gustavo [EMAIL PROTECTED] wrote: Dear GROMACS Users, I'm trying to use GROMACS to get some MD snapshots for single-point quantum mechanical calculations, trying to observe HOMO-LUMO gap of a protein immersed in water with counterions, at a given salt concentration (4600 atoms in total). I'd like to know if they are reliable enough to send to QM calculations. I've got two questions: Which are the criteria I should be looking at? And one of them I've analyzed was energy conservation (I'm doing 300K NVT MD, with 10A cutoff for vdw and coulomb, with PME electrostatics, and double precision), and the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but I've got 0.3-0.5 in all simulations I've done. What should I do? This is because of T coupling. If you turn off T coupling it will be better (but you will not have constant T, and the energy will dirft in the long run). Your starting structures are fine for QM, but QM minimization will take a LONG time. Thanks in advance, Gustavo Troiano Feliciano This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] xtc error
luciano.pgomes wrote: Hi, Hi All, I had this problem running MD on a single Debian machine: Program mdrun_d, VERSION 3.3.1 Source code file: stat.c, line: 257 Fatal error: XTC error There is no chance of being size exceeded of file or quota, or disk error. I compiled gromacs with gcc-3.4... Does anyone know what this error means? Gcc version may be the cause? Thanks, Luciano P Gomes it can also mean that your system is exploding. No. The xtc file doesn't opened. It crashed VMD. I forgot saying that I was running simulated annealing protocol with a DNA molecule and crystallographic water molecules (HOH) freezed, only moving ions and water molecules placed by genbox (tip3p). The crash occured on 2 ps of simulation time in a temperature of 50K. I had excluded non-bonded interactions: DNA DNA HOH DNA HOH HOH. I am running now a simple MD at 300K and this error haven't occured yet. I am trying to understand... did you use pressure coupling? you can not have Pcoupl with freezing and constraints. Thanks, Luciano ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] limit on energygrp_table
Thanks for your suggestions, I have gone for the solution where I change the type of group numbers from uchars to unsigned short. It seems however that this solution is not very elegant: I fail to understand the logic of limiting the number of groups in the energygrp_table field to 254. Indeed the energygrp_table field is made of pairs of groups. So if the group numbers are stored as uchar the number of possible pairwise interactions between those groups is much greater than 254 (of the order of 2^16 and not 2^8). I am actually in that case: I have not too many groups (~20) so I can store all the numbers in a uchar but when I generate all possible pairwise interactions I have to input something like 400 group names under energygrp_table and then grompp complains. -Is there a way to increase this limit (by changing a constant and then recompile) ? or is it more complicated (from the value 254 one could guess that there is some one one-byte optimization) This is indeed a on-byte optimization. The group numbers are stored as uchars (include/types/atoms.h). You could change this, then you also have to change 2 or more other files for the io and communication of these numbers. I have modified include/types/atoms.h Then it seemed logical to also change the following lines in src/kernel/readir.c #define MAXPTR 65534 #define NOGID 65535 to account for the new limits. I can compile the modified code and run grompp without a warning on my system. The only strange thing is that grompp complains if I do not provide tablep*.xvg files even though I want to use the same tabulated potentials for my inter and intra (defined through some pairs) molecular non-bonded potentials. Nevertheless when I try to run some energy minimization it directly complains that my first 1-4 interaction is beyond table range of 0 nm,... and will ignore all 1-4 (i assume it means pairs). This message seems really odd,... especially the 0nm part. I have probably to propagate the change of type to more files. I welcome all suggestions. Adrien. -- Adrien Leygue Department of Materials Science and Engineering School of Chemical Engineering National Technical University of Athens 9 Heroon Polytechniou Street Zografou Campus, Athens 157 80, GREECE Tel/Fax: +30210 772-3112 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problems prior to running lipid-protein simulation
Dear All; when I try to run pdb2gmx command for making .top file of POPC+Protein, an error appears: Residue 'POPC' not found in residue topology database. I have copied all necessary .itp files in share folder and also in the path where it is run. what could be the problem and how to solve it? (I have passed these steps long time ago but now I am not able to reproduce the procedure!) thanks; Adak Nasiripour. - Check out the hottest 2008 models today at Yahoo! Autos.___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulating hydrocarbons in water
Much appreciated, works beautifully! On 10/10/07, TJ Piggot [EMAIL PROTECTED] wrote: Just as a note editconf will covert a pdb to a gro file Tom --On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser [EMAIL PROTECTED] wrote: Yes I tried this and it doesn't work for me. I get: Fatal error: Library file ffG53a6.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script that converts pdb to gro, and I still get the above error. -Adam On 10/10/07, David van der Spoel [EMAIL PROTECTED] wrote: Adam Fraser wrote: Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I've built topologies for hexadecane compatible with NAMD, so I figure I should be able to do the same in Gromacs but I'm fuzzy on how to go about doing so (what files to edit). I was also hoping to get some input on which forcefield would be best for this sort of system. I'd greatly appreciate it if someone could give me some pointers on how to get started here. Thanks very much, Adam if you have a pdb file you can run x2top (3.3.2 only). ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulating hydrocarbons in water
Ah, okay thanks very much! I thought-sure I had the most recent version, but apparently not. Still there's one quirk... x2top -f HexA.gro -o HexA.top -r HexA.rtp -alldih ...This works to generate a topology file, but still, the program is seg-faulting before writing out the residue type file (*.rtp). I'm not yet sure if I can get by without the .rtp since hexadecane (C16) won't likely be a recognized residue type. Any ideas why this is seg-faulting or how I can get around the fact that restype (C16) won't be recognized? Thanks so much, -Adam On 10/10/07, David van der Spoel [EMAIL PROTECTED] wrote: Adam Fraser wrote: Yes I tried this and it doesn't work for me. I get: Fatal error: Library file ffG53a6.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) did you use 3.3.2 ? The default and only supported FF there is OPLS. For GROMOS variants you can try the prodrg webserver. Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script that converts pdb to gro, and I still get the above error. -Adam On 10/10/07, * David van der Spoel* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Adam Fraser wrote: Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I've built topologies for hexadecane compatible with NAMD, so I figure I should be able to do the same in Gromacs but I'm fuzzy on how to go about doing so (what files to edit). I was also hoping to get some input on which forcefield would be best for this sort of system. I'd greatly appreciate it if someone could give me some pointers on how to get started here. Thanks very much, Adam if you have a pdb file you can run x2top (3.3.2 only). ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] mailto:[EMAIL PROTECTED][EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] 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 [EMAIL PROTECTED] 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
[gmx-users] Re:gmx-users Digest, Vol 42, Issue 36
HI David, I used -DPOSRE, no constraints but temperature coupling (berendsen), no pressure coupling. thanks, Luciano luciano.pgomes wrote: Hi, Hi All, I had this problem running MD on a single Debian machine: Program mdrun_d, VERSION 3.3.1 Source code file: stat.c, line: 257 Fatal error: XTC error There is no chance of being size exceeded of file or quota, or disk error. I compiled gromacs with gcc-3.4... Does anyone know what this error means? Gcc version may be the cause? Thanks, Luciano P Gomes it can also mean that your system is exploding. No. The xtc file doesn't opened. It crashed VMD. I forgot saying that I was running simulated annealing protocol with a DNA molecule and crystallographic water molecules (HOH) freezed, only moving ions and water molecules placed by genbox (tip3p). The crash occured on 2 ps of simulation time in a temperature of 50K. I had excluded non-bonded interactions: DNA DNA HOH DNA HOH HOH. I am running now a simple MD at 300K and this error haven't occured yet. I am trying to understand... did you use pressure coupling? you can not have Pcoupl with freezing and constraints. Thanks, Luciano ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Problems prior to running lipid-protein simulation
Dear Adak, [EMAIL PROTECTED] wrote: Dear All; when I try to run pdb2gmx command for making .top file of POPC+Protein, an error appears: Residue 'POPC' not found in residue topology database. I have copied all necessary .itp files in share folder and also in the path where it is run. what could be the problem and how to solve it? (I have passed these steps long time ago but now I am not able to reproduce the procedure!) thanks; Adak Nasiripour. I think the process you might be wanting to perform is to run pdb2gmx for your protein only (with suitably adjusted coordinates so that it matches your bilayer coordinates) and then add #include lines to the resulting topology to add in the POPC part *after* the force field #include statement: #include ffgmx.itp #include lipids.itp #include popc.itp - assuming that these are your .itp file names. Then adjust the [ molecules ] section to list the number and type of your components and you should have a working .top file. You don't have to run pdb2gmx for the whole system at any point (it's not going to work anyway unless you add the POPC parameters to all the force field files and then add the POPC residue to the .rtp file so that pdb2gmx can recognize it). Cheers, Bruce -- Hamewith - the road that's never dreary Dr. Bruce F. Milne CEQOFFUP Faculdade de Farmácia Universidade do Porto Rua Aníbal Cunha - 164 4050-047 Porto Portugal email: [EMAIL PROTECTED] ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Criteria and Energy Conservation
Well, yeah. But I want to look at the HOMO-LUMO gap of the system in the living environment. Since the system is too big to do MD with the QM code, I tried to use the best force field description I could, and the smallest box as well, to get structures that could represent the system at 300K. And the forces from QM are not so bad so far, within the order I'd expect from MD with the QM code. Anyway, thanks very much for the hints so far, David, and if you have some suggestion or anything at all to add, feel free to do so. [EMAIL PROTECTED] wrote: Thank you very much again, David! Then it's fine for me, since what I want to do is a single point QM in termalized snapshots of the dynamics and not QM minimization. But then you will get systematically incorrect energies due to weird (force field dependent) bond lengths etc. Gustavo [EMAIL PROTECTED] wrote: Dear GROMACS Users, I'm trying to use GROMACS to get some MD snapshots for single-point quantum mechanical calculations, trying to observe HOMO-LUMO gap of a protein immersed in water with counterions, at a given salt concentration (4600 atoms in total). I'd like to know if they are reliable enough to send to QM calculations. I've got two questions: Which are the criteria I should be looking at? And one of them I've analyzed was energy conservation (I'm doing 300K NVT MD, with 10A cutoff for vdw and coulomb, with PME electrostatics, and double precision), and the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but I've got 0.3-0.5 in all simulations I've done. What should I do? This is because of T coupling. If you turn off T coupling it will be better (but you will not have constant T, and the energy will dirft in the long run). Your starting structures are fine for QM, but QM minimization will take a LONG time. Thanks in advance, Gustavo Troiano Feliciano This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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
RE: [gmx-users] Problems prior to running lipid-protein simulation
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_ residue_topology_database You only run pdb2gmx on molecules that you want to generate a topology file for. For the lipids, you will already have the .itp files for it, or should have. So you don't run pdb2gmx on it. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dummies usage doubts
Jones de Andrade wrote: Hi all. Well, I'm having a bit of trouble here because the work has decided to go in the direction of something I've never used before with gromacs: dummy atoms (or now virtual sites). I assume this is not for a protein, in which case pdb2gmx does it for you. I've got at least three questions in order to use them: 1 - does the virtual sites need to be included in the .gro files in order to make a simulation run? Yes. 2 - do I need to include them in the exclusion list? It depends, but usually yes. 3 - do I need to include them in the atoms section? Yes. Thanks a lot in advance for any help anyone can provide in these subjects. ;) Check the mannual too. Chapter 5. An dtopologies for TIP4P, TIP5P etc. Sincerally yours, Jones ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
