Re: [gmx-users] Arginine_Hydrochloride topology
shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] re-equilbrating membrane protein system after g_membed and ligand addition
I was looking at the g_membed paper recently, and noticed the authors only spent 10ns to re-equilibrate the membedded-system after g_membeding. This they also did after bumping the temperature from 300 to 323K to prevent ordering of the bilayer even though the typical simulation temperatures of POPC is 300 to 310K...Anyone know why 323K was used? Was it to compare it to the DOPC environment or something? I noticed for my particular system, I had to run a round of EM on the post-membedded system in order to resolve some clashes before I could mdrun. Then I ran 10ns in NPT with gen_vel=yes at 310K and position restraints on the helix CA atoms. I am inferring that because the membrane patch I used had been previously equilibrated after I constructed it and ran it under NPT at 300K for 100ns, 10ns should be sufficient time to re-equilibrate with the protein in the middle and 310K temperature? After the 10ns with protein restrained, I ran Grid_MAT on it and got a reasonable APL (61-62A^2/lipid when taking protein atoms into account, comparable to pre-g_membed patch) and the box dimensions look stable. Is this sufficient to answer the abvove question? Now I am going to be introducing a ligand to the protein. Is there a way to preserve any state, like velocities of all the previous atoms? I was thinking of the doing the EM while freezing everything but the ligand atoms and allowing the ligand to change conformation (like a docking refinement). After this, can I have the thermostat and barostat rescale the original velocities (and gradually heat the ligand) instead of reinitialising everything? -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] re-equilbrating membrane protein system after g_membed and ligand addition
Peter C. Lai wrote: I was looking at the g_membed paper recently, and noticed the authors only spent 10ns to re-equilibrate the membedded-system after g_membeding. This they also did after bumping the temperature from 300 to 323K to prevent ordering of the bilayer even though the typical simulation temperatures of POPC is 300 to 310K...Anyone know why 323K was used? Was it to compare it to the DOPC environment or something? I can't comment on this, but it seems odd to me, too. I noticed for my particular system, I had to run a round of EM on the post-membedded system in order to resolve some clashes before I could mdrun. Then I ran 10ns in NPT with gen_vel=yes at 310K and position restraints on the helix CA atoms. I am inferring that because the membrane patch I used had been previously equilibrated after I constructed it and ran it under NPT at 300K for 100ns, 10ns should be sufficient time to re-equilibrate with the protein in the middle and 310K temperature? I generally find that membrane protein systems need at least 20 ns or so to really be equilibrated, but perhaps your system is a bit different. 10 ns is about the shortest time you can use to start seeing translational relaxation (rotational relaxation of lipids is shorter, roughly 5 ns). After the 10ns with protein restrained, I ran Grid_MAT on it and got a reasonable APL (61-62A^2/lipid when taking protein atoms into account, comparable to pre-g_membed patch) and the box dimensions look stable. Is this sufficient to answer the abvove question? Could be. Seems reasonable. Now I am going to be introducing a ligand to the protein. Is there a way to preserve any state, like velocities of all the previous atoms? I was thinking of the doing the EM while freezing everything but the ligand atoms and allowing the ligand to change conformation (like a docking refinement). After this, can I have the thermostat and barostat rescale the original velocities (and gradually heat the ligand) instead of reinitialising everything? I doubt it. By introducing new atoms into the system, you can't use a checkpoint file any more so you lose the state you had before. You can preserve velocities in a .gro file, but I can't think of a reasonable way to have those read (while not having velocities for the ligand) and then heat up the ligand. You'd have to use gen_vel = no in conjunction with simulated annealing, which sounds like a recipe for instability. Is there any particular reason you think a specific set of velocities is required? Random sampling is all part of running proper simulations, so you need multiple, independent states to converge to get a reliable result, anyway. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] re-equilbrating membrane protein system after g_membed and ligand addition
On 2011-07-29 07:25:08AM -0500, Justin A. Lemkul wrote: Peter C. Lai wrote: I was looking at the g_membed paper recently, and noticed the authors only spent 10ns to re-equilibrate the membedded-system after g_membeding. This they also did after bumping the temperature from 300 to 323K to prevent ordering of the bilayer even though the typical simulation temperatures of POPC is 300 to 310K...Anyone know why 323K was used? Was it to compare it to the DOPC environment or something? I can't comment on this, but it seems odd to me, too. I noticed for my particular system, I had to run a round of EM on the post-membedded system in order to resolve some clashes before I could mdrun. Then I ran 10ns in NPT with gen_vel=yes at 310K and position restraints on the helix CA atoms. I am inferring that because the membrane patch I used had been previously equilibrated after I constructed it and ran it under NPT at 300K for 100ns, 10ns should be sufficient time to re-equilibrate with the protein in the middle and 310K temperature? I generally find that membrane protein systems need at least 20 ns or so to really be equilibrated, but perhaps your system is a bit different. 10 ns is about the shortest time you can use to start seeing translational relaxation (rotational relaxation of lipids is shorter, roughly 5 ns). Well I picked 10ns since the authors of g_membed claim that their g_membed packs so well (at least compared to say, inflateGRO) *shrug*. In fact, they claim that you can re-equilbrate in only 1ns after g_membed. In addition to APL, they measured deuterium order parameter and the density profile of water in z-axis columns, but they didn't elaborate on these other 2 metrics... After the 10ns with protein restrained, I ran Grid_MAT on it and got a reasonable APL (61-62A^2/lipid when taking protein atoms into account, comparable to pre-g_membed patch) and the box dimensions look stable. Is this sufficient to answer the abvove question? Could be. Seems reasonable. Now I am going to be introducing a ligand to the protein. Is there a way to preserve any state, like velocities of all the previous atoms? I was thinking of the doing the EM while freezing everything but the ligand atoms and allowing the ligand to change conformation (like a docking refinement). After this, can I have the thermostat and barostat rescale the original velocities (and gradually heat the ligand) instead of reinitialising everything? I doubt it. By introducing new atoms into the system, you can't use a checkpoint file any more so you lose the state you had before. You can preserve velocities in a .gro file, but I can't think of a reasonable way to have those read (while not having velocities for the ligand) and then heat up the ligand. You'd have to use gen_vel = no in conjunction with simulated annealing, which sounds like a recipe for instability. Is there any particular reason you think a specific set of velocities is required? Random sampling is all part of running proper simulations, so you need multiple, independent states to converge to get a reliable result, anyway. Yeah didn't think so, but worth a thought. Just trying to look ways to save computational time. Wolf et al (the g_membed authors) seem to suggest that if the structure is already close-to or at equilibrium, then it should take little to to re-equilibrate when you have minimal perturbation... -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv problem for two groups
Liu Shiyong wrote: Dear all, I tried to output protein-ligand complex from trr file . Could I select both Group 2 and Group 12 at the same time ? Or I have to run this command for every group , respectively? Use make_ndx to merge the groups and pass the index file to trjconv. -Justin Select group for output Opening library file /usr/share/gromacs/top//aminoacids.dat Group 0 ( System) has 253787 elements Group 1 ( Protein) has 3403 elements Group 2 ( Protein-H) has 2655 elements Group 3 ( C-alpha) has 328 elements Group 4 (Backbone) has 984 elements Group 5 ( MainChain) has 1313 elements Group 6 (MainChain+Cb) has 1623 elements Group 7 ( MainChain+H) has 1627 elements Group 8 ( SideChain) has 1776 elements Group 9 ( SideChain-H) has 1342 elements Group10 ( Prot-Masses) has 3403 elements Group11 ( Non-Protein) has 250384 elements Group12 ( DRG) has28 elements Group13 ( SOL) has 250356 elements Group14 ( Other) has 250384 elements Select a group: Best Shiyong -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 --- -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Dimensionless units question
Hi all, I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which consists of a lattice of 25 evenly spaced charges in the xy plane and a single charge in the center above to preserve charge neutrality. The reference values I have been given are in dimensionless units, so I am tasked with either converting my output to dimensionless units or having gromacs work in reduced units from the get go. I have set the mass of each charge to 1, the magnitude of the charge on each particle to 1, and the values of the C6 and C12 parameters in my itp file to 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. I've turned off temperature coupling because this is purely a test of the handling of electrostatics with 3D Ewald summation plus the correction for slab geometry. However, the force and energy I calculate are still quite far from the reference values. Have I missed anything if I want my output to be in dimensionless units? Thanks, Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] PRODRG tools
Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. Best Shiyong -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PRODRG tools
Liu Shiyong wrote: Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. You can contact the maintainers for a standalone version of PRODRG. Then you can run it whenever you want. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dimensionless units question
Hi, reduced units works for LJ particles only. I am not sure if it works when you include electrostatics. When you set charge = 1 it is 1electronic charge. I would suggest not to use the reduced units for LJ in this scenario. Amit On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall amars...@uwo.ca wrote: Hi all, I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which consists of a lattice of 25 evenly spaced charges in the xy plane and a single charge in the center above to preserve charge neutrality. The reference values I have been given are in dimensionless units, so I am tasked with either converting my output to dimensionless units or having gromacs work in reduced units from the get go. I have set the mass of each charge to 1, the magnitude of the charge on each particle to 1, and the values of the C6 and C12 parameters in my itp file to 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. I've turned off temperature coupling because this is purely a test of the handling of electrostatics with 3D Ewald summation plus the correction for slab geometry. However, the force and energy I calculate are still quite far from the reference values. Have I missed anything if I want my output to be in dimensionless units? Thanks, Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dimensionless units question
Hi Amit, So if I understand you correctly, any LJ interaction I impose on these particles will be quite arbitrary because I'm only concerned with electrostatics, right? How then might I go about comparing the dimensionless reference values given with the values I calculated? I don't think I can simply compare their ratios, as there would still be a unit of length to deal with. Thanks, Alex On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey kgp.a...@gmail.com wrote: Hi, reduced units works for LJ particles only. I am not sure if it works when you include electrostatics. When you set charge = 1 it is 1electronic charge. I would suggest not to use the reduced units for LJ in this scenario. Amit On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall amars...@uwo.ca wrote: Hi all, I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which consists of a lattice of 25 evenly spaced charges in the xy plane and a single charge in the center above to preserve charge neutrality. The reference values I have been given are in dimensionless units, so I am tasked with either converting my output to dimensionless units or having gromacs work in reduced units from the get go. I have set the mass of each charge to 1, the magnitude of the charge on each particle to 1, and the values of the C6 and C12 parameters in my itp file to 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. I've turned off temperature coupling because this is purely a test of the handling of electrostatics with 3D Ewald summation plus the correction for slab geometry. However, the force and energy I calculate are still quite far from the reference values. Have I missed anything if I want my output to be in dimensionless units? Thanks, Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dimensionless units question
I am not sure what you want to measure. You mentioned that force and energy I calculate are still quite far from the reference values, now are you only looking at electrostatic contributions to these or the total contributions? If its total contribution then LJ parameters should also be correct and for that you should switch to standard gromacs units. Also why do you need to use gmx.ff, seems to me that you already have the parameters (ie the LJ parameters and charges) On Fri, Jul 29, 2011 at 11:30 AM, Alex Marshall amars...@uwo.ca wrote: Hi Amit, So if I understand you correctly, any LJ interaction I impose on these particles will be quite arbitrary because I'm only concerned with electrostatics, right? How then might I go about comparing the dimensionless reference values given with the values I calculated? I don't think I can simply compare their ratios, as there would still be a unit of length to deal with. Thanks, Alex On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey kgp.a...@gmail.com wrote: Hi, reduced units works for LJ particles only. I am not sure if it works when you include electrostatics. When you set charge = 1 it is 1electronic charge. I would suggest not to use the reduced units for LJ in this scenario. Amit On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall amars...@uwo.ca wrote: Hi all, I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which consists of a lattice of 25 evenly spaced charges in the xy plane and a single charge in the center above to preserve charge neutrality. The reference values I have been given are in dimensionless units, so I am tasked with either converting my output to dimensionless units or having gromacs work in reduced units from the get go. I have set the mass of each charge to 1, the magnitude of the charge on each particle to 1, and the values of the C6 and C12 parameters in my itp file to 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. I've turned off temperature coupling because this is purely a test of the handling of electrostatics with 3D Ewald summation plus the correction for slab geometry. However, the force and energy I calculate are still quite far from the reference values. Have I missed anything if I want my output to be in dimensionless units? Thanks, Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dimensionless units question
I'm trying to calculate the total electrostatic energy of the system, and the force in the Z direction on the particle placed above the lattice. It's a purely electrostatic problem, ideally LJ shouldn't come into it at all, but I don't know how else to convert the resulting energy and force to dimensionless units, which I must do because I was given reference values in dimensionless units. I guess I'm not actually using gmx.ff, I was just using the C6-C12 convention for LJ parameters used in that forcefield's ffnonbonded.itp. On Fri, Jul 29, 2011 at 3:50 PM, Amit Choubey kgp.a...@gmail.com wrote: I am not sure what you want to measure. You mentioned that force and energy I calculate are still quite far from the reference values, now are you only looking at electrostatic contributions to these or the total contributions? If its total contribution then LJ parameters should also be correct and for that you should switch to standard gromacs units. Also why do you need to use gmx.ff, seems to me that you already have the parameters (ie the LJ parameters and charges) On Fri, Jul 29, 2011 at 11:30 AM, Alex Marshall amars...@uwo.ca wrote: Hi Amit, So if I understand you correctly, any LJ interaction I impose on these particles will be quite arbitrary because I'm only concerned with electrostatics, right? How then might I go about comparing the dimensionless reference values given with the values I calculated? I don't think I can simply compare their ratios, as there would still be a unit of length to deal with. Thanks, Alex On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey kgp.a...@gmail.com wrote: Hi, reduced units works for LJ particles only. I am not sure if it works when you include electrostatics. When you set charge = 1 it is 1electronic charge. I would suggest not to use the reduced units for LJ in this scenario. Amit On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall amars...@uwo.ca wrote: Hi all, I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which consists of a lattice of 25 evenly spaced charges in the xy plane and a single charge in the center above to preserve charge neutrality. The reference values I have been given are in dimensionless units, so I am tasked with either converting my output to dimensionless units or having gromacs work in reduced units from the get go. I have set the mass of each charge to 1, the magnitude of the charge on each particle to 1, and the values of the C6 and C12 parameters in my itp file to 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. I've turned off temperature coupling because this is purely a test of the handling of electrostatics with 3D Ewald summation plus the correction for slab geometry. However, the force and energy I calculate are still quite far from the reference values. Have I missed anything if I want my output to be in dimensionless units? Thanks, Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dimensionless units question
On Fri, Jul 29, 2011 at 12:14 PM, Alex Marshall amars...@uwo.ca wrote: I'm trying to calculate the total electrostatic energy of the system, and the force in the Z direction on the particle placed above the lattice. It's a purely electrostatic problem, ideally LJ shouldn't come into it at all, but I don't know how else to convert the resulting energy and force to dimensionless units, which I must do because I was given reference values in dimensionless units. Why not use 0 for LJ parameters? You will have to figure out the units of energy and force in the reference otherwise you cannot make the comparison. I guess I'm not actually using gmx.ff, I was just using the C6-C12 convention for LJ parameters used in that forcefield's ffnonbonded.itp. On Fri, Jul 29, 2011 at 3:50 PM, Amit Choubey kgp.a...@gmail.com wrote: I am not sure what you want to measure. You mentioned that force and energy I calculate are still quite far from the reference values, now are you only looking at electrostatic contributions to these or the total contributions? If its total contribution then LJ parameters should also be correct and for that you should switch to standard gromacs units. Also why do you need to use gmx.ff, seems to me that you already have the parameters (ie the LJ parameters and charges) On Fri, Jul 29, 2011 at 11:30 AM, Alex Marshall amars...@uwo.ca wrote: Hi Amit, So if I understand you correctly, any LJ interaction I impose on these particles will be quite arbitrary because I'm only concerned with electrostatics, right? How then might I go about comparing the dimensionless reference values given with the values I calculated? I don't think I can simply compare their ratios, as there would still be a unit of length to deal with. Thanks, Alex On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey kgp.a...@gmail.comwrote: Hi, reduced units works for LJ particles only. I am not sure if it works when you include electrostatics. When you set charge = 1 it is 1electronic charge. I would suggest not to use the reduced units for LJ in this scenario. Amit On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall amars...@uwo.ca wrote: Hi all, I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which consists of a lattice of 25 evenly spaced charges in the xy plane and a single charge in the center above to preserve charge neutrality. The reference values I have been given are in dimensionless units, so I am tasked with either converting my output to dimensionless units or having gromacs work in reduced units from the get go. I have set the mass of each charge to 1, the magnitude of the charge on each particle to 1, and the values of the C6 and C12 parameters in my itp file to 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. I've turned off temperature coupling because this is purely a test of the handling of electrostatics with 3D Ewald summation plus the correction for slab geometry. However, the force and energy I calculate are still quite far from the reference values. Have I missed anything if I want my output to be in dimensionless units? Thanks, Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
Re: [gmx-users] PRODRG tools
Actually, you can use other parametrization tools like antechamber (for amber) or cgenff (for charmm). Liu Shiyong wrote: Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. You can contact the maintainers for a standalone version of PRODRG. Then you can run it whenever you want. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] cannot open file
Hi gromacs users, I'm running a simulation but I keep getting the following errors. rogram mdrun_mpi, VERSION 4.5.1 Source code file: gmxfio.c, line: 537 Can not open file: taExcited.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That Was Cool (Beavis and Butthead) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 4 -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- gcq#182: That Was Cool (Beavis and Butthead) -- mpirun has exited due to process rank 0 with PID 9680 on node compute-0-10 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). I don't know why gromacs cannot find my taExcited.tpr file, since it does exist in my working directory. However I noticed that when gromacs makes copies of my log files, its putting it in my home directory. This leads me to believe that it must be looking into the wrong path. This problem is only recent since gromacs knows where to looking when i reference my other working files, such as when i run grompp, but mdrun does not want to open up my .tpr file. Any ideas? Thanks, Taylor Kaplan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] umbrella sampling
Hi, I used umbrella sampling method to restrain the distance of two molecules at several distances. Then I can use g_wham to get the free energy as a function of the distance. Is there any way that I can get the free energy as a function of another parameter? Thanks a lot. Sincerely, Qian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] umbrella sampling
Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Thursday, August 4, 2011. For all questions about CloudBroker and the CloudBroker Platform, please contact the company under i...@cloudbroker.com or Nicola Fantini under nicola.fant...@cloudbroker.com. If you need to talk to me in person for urgent or important issues, please call my mobile phone number. Kind regards, Wibke Sudholt -- Dr. Wibke Sudholt CEO CloudBroker GmbH Technoparkstrasse 1 CH-8005 Zurich Switzerland Phone: +41 44 633 79 34 Email: i...@cloudbroker.com Web:http://www.cloudbroker.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] umbrella sampling
Qian Wang wrote: Hi, I used umbrella sampling method to restrain the distance of two molecules at several distances. Then I can use g_wham to get the free energy as a function of the distance. Is there any way that I can get the free energy as a function of another parameter? Thanks a lot. Please define what the other parameter is. Right now the only answer is maybe, maybe not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] cannot open file
Taylor Kaplan wrote: Hi gromacs users, I'm running a simulation but I keep getting the following errors. rogram mdrun_mpi, VERSION 4.5.1 Source code file: gmxfio.c, line: 537 Can not open file: taExcited.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That Was Cool (Beavis and Butthead) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 4 -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- gcq#182: That Was Cool (Beavis and Butthead) -- mpirun has exited due to process rank 0 with PID 9680 on node compute-0-10 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). I don't know why gromacs cannot find my taExcited.tpr file, since it does exist in my working directory. However I noticed that when gromacs makes copies of my log files, its putting it in my home directory. This leads me to believe that it must be looking into the wrong path. This problem is only recent since gromacs knows where to looking when i reference my other working files, such as when i run grompp, but mdrun does not want to open up my .tpr file. Any ideas? Are you submitting the job to a queue? If so, please provide the entire script you're using to execute mdrun. Does the problem persist in newer versions of Gromacs? It's always best to start from the newest available version, rather than troubleshoot an old one, just to find out the problem has already been resolved. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] citation
Hello all, Can anyone tell me how gromacs may be cited besides Principal Papers 1. Berendsen, et al. (1995) *Comp. Phys. Comm.* *91: *43-56. (DOIhttp://dx.doi.org/doi:10.1016/0010-4655%2895%2900042-E_, Citations of this paperhttp://scholar.google.com/scholar?cites=6703762643559347673hl=en ) 2. Lindahl, et al. (2001) *J. Mol. Model.* *7:* 306-317. (DOIhttp://dx.doi.org/10.1007/s008940100045, Citations of this paperhttp://scholar.google.com/scholar?cites=135270318718960hl=en ) 3. van der Spoel, et al. (2005) *J. Comput. Chem.* *26:* 1701-1718. (DOIhttp://dx.doi.org/10.1002/jcc.20291, Citations of this paperhttp://scholar.google.com/scholar?cites=8599454604037079587hl=en ) 4. Hess, et al. (2008) *J. Chem. Theory Comput.* *4:* 435-447. (DOIhttp://dx.doi.org/10.1021/ct700301q, Citations of this paperhttp://scholar.google.com/scholar?cites=15361472353040457616hl=en ) I am using oplsaa and found ; References for the OPLS-AA force field: ; ; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, ; J. Am. Chem. Soc. 118, 11225-11236 (1996). ; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998). ; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998). ; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999). ; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001). ; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001). ; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J. Phys. Chem. B 105, 6474 (2001). ; Do I have to include all these or some of them can be skipped? Citations depend on specific features ( e.g free energy calculations, ...) that have been utilized or the above references are sufficient? Am I missing anything? Thank you, Best -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] citation
Elisabeth wrote: Hello all, Can anyone tell me how gromacs may be cited besides Principal Papers 1. Berendsen, et al. (1995) /Comp. Phys. Comm./ *91: *43-56. (DOI http://dx.doi.org/doi:10.1016/0010-4655%2895%2900042-E_, Citations of this paper http://scholar.google.com/scholar?cites=6703762643559347673hl=en) 2. Lindahl, et al. (2001) /J. Mol. Model./ *7:* 306-317. (DOI http://dx.doi.org/10.1007/s008940100045, Citations of this paper http://scholar.google.com/scholar?cites=135270318718960hl=en) 3. van der Spoel, et al. (2005) /J. Comput. Chem./ *26:* 1701-1718. (DOI http://dx.doi.org/10.1002/jcc.20291, Citations of this paper http://scholar.google.com/scholar?cites=8599454604037079587hl=en) 4. Hess, et al. (2008) /J. Chem. Theory Comput./ *4:* 435-447. (DOI http://dx.doi.org/10.1021/ct700301q, Citations of this paper http://scholar.google.com/scholar?cites=15361472353040457616hl=en) What else are you looking for? These are the principal papers, of which you should cite at least one (probably the one that pertains to the Gromacs version you're using). I am using oplsaa and found ; References for the OPLS-AA force field: ; ; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, ; J. Am. Chem. Soc. 118, 11225-11236 (1996). ; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998). ; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998). ; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999). ; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001). ; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001). ; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J. Phys. Chem. B 105, 6474 (2001). ; Do I have to include all these or some of them can be skipped? Citations depend on specific features ( e.g free energy calculations, ...) that have been utilized or the above references are sufficient? Am I missing anything? If you're not sure, you should read the papers. Many of these pertain to specific functional groups and molecules that for which parameters were derived (see atomtypes.atp for instance). If you did not utilize these groups, then citing that particular paper would be unnecessary. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] umbrella sampling
format your data for 2D-WHAM with 1D being the distance and the 2nd-D being your other coordinate of interest. Specify a value of zero for the force constants for your 2nd-D. Run 2D-WHAM. Boltzmann project the 2D PMF onto your 2nd-D. I think you can also do essentially the same thing by re-weighting using the F-values from 1D-WHAM, but I find the above method to be the simplest. It also provides you with a 2D free energy profile, which can be informative both biologically and to indicate on sampling problems. Note that you're very likely going to run into convergence problems since your 2nd-D will rely on brute-force to converge, and worse: the umbrellas in 1D can force the sampling in the 2nd-D to surmount energy barriers that might be circumvented in unrestrained sampling. Chris. -- original message -- Qian Wang wrote: Hi, I used umbrella sampling method to restrain the distance of two molecules at several distances. Then I can use g_wham to get the free energy as a function of the distance. Is there any way that I can get the free energy as a function of another parameter? Thanks a lot. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] OPLSAA parameters
Hello to all, I am looking for bonded and nonbonded parameters for C H atoms in saturated hydrocarbons. atom types are: Carbon atoms opls_135 opls_136 H opls_140 opls_135 12.01100 ; alkane CH3 opls_136 12.01100 ; alkane CH2 opls_1401.00800 ; alkane H. Please help me out with the following: - I am wondering if I am selecting the correct values, for C-C and C-H bonds from ffoplsaabon.itp. C C 10.15100 292880.0 ; wlj oxalic acid, etc. HCC 10.10900 284512.0 ; wlj 7/96 - what does wlj mean? - what are the units? Angle CA CA CZ 1 120.000585.760 ; wlj CA CA CR 1 120.000527.184 ; CA CA CX 1 120.000711.280 ; C CT Cl 1 109.800577.392 ; wlj - I can not distinguish CA CZ What are they referring to? [ dihedraltypes ] C C CT HC 3 0.17782 0.53346 0.0 -0.71128 0.0 0.0 ; dicarbonyls BMC 8,1881(2000) - Is this what I need for oplsaa 135 136 140? ffoplsaanb.itp. opls_135 CT6 12.01100-0.180 A3.5e-01 2.76144e-01 opls_136 CT6 12.01100-0.120 A3.5e-01 2.76144e-01 opls_140 HC1 1.00800 0.060 A2.5e-01 1.25520e-01 - are these parameters for opls_135 12.01100 ; alkane CH3 opls_136 12.01100 ; alkane CH2 opls_1401.00800 ; alkane H. ? Also in usr/local/gromacs/share/gromacs/top/ directory I can not find ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in previous versions these files were accessible. I am using itp files from version 4.0.7 and wanted to make sure the above parameters for oplsa_135 oplsa_136 and oplsa_140 have been remained unchanged in 4.5.4. Where can I find these files? Thanks, Regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
