[gmx-users] tau_t and tc_grps for v-rescale (2)
Hi again, I posted yesterday the query below, but have not received any feedback up to now. I would like to put my question in another way: in Justin's CAP-15 in DPPC tutorial he uses during NVT equilibration Bussi's thermostat (V-rescale) together with three separate coupling groups: ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein DPPC SOL_CL ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K), Is this separate coupling needed at all taking into account that this temperature coupling method produces the correct coupling? Is it probably better to use a single coupling constant (system) and so avoid problems using this artificial correction to deal with the hot solvent / cold solute artifact? Could somebody kindly tell me how large could the coupling constant, tau_t, be? Is it OK to switch, e.g., from 0.1 to 0.3 ps after T equilibration is reached, i.e., during the production phase? Many thanks again in advance and kind regards, Felipe On 09/27/2012 03:49 PM, Felipe Pineda, PhD wrote: Hi, I'd greatly appreciate any general advice on the possibility to use several (2 or more) tc_grps with v-rescale and how large could be tau_t with this coupling method (is 0.3 ps still OK?). Many thanks in advance and best regards, Felipe -- 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] doubt in minimization part
Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now I am confusing with the following ( shown at botom) part of the tutorial.Here minimization means to minimize system_inflated.gro, is it right? Then without .epr and .top files of system_inflated.gro how can I do this? perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat -- 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] Exclusions in TIP4P
Hi all, In the OPLS-AA tip4p.itp file I see: [ moleculetype ] ; molname nrexcl SOL 2 and [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 If bonded interactions are included (FLEXIBLE defined), interactions between atoms 1, 2, 3 are already excluded, right? And is it needed to have both the n-m and m-n exclusions listed? Wouldn't it be the same with this?: [ exclusions ] 1 2 3 4 2 3 4 3 4 Thanks, Ignacio -- 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] g_tcaf segmentation fault
I check my .mdp setting and you were right. I haven't been saving the velocities in my .trr file. I change my setting and everything worked fine. Thanks for your help Stelios On 09/27/2012 03:37 PM, Tsjerk Wassenaar wrote: Re: [gmx-users] g_tcaf segmentation fault The .trr file can contain coordinates, velocities, and forces over time, depending on your .mdp settings (nstxout, nstvout, nstfout). For g_tcaf, you need to have velocities. It does say so in the manpage. Run gmxcheck to see what's in your .trr file. A segmentation fault with the analysis tools is usually an indication that there is a mismatch in data, e.g. between trajectory and reference structure, or that some data is missing, like velocities in a trajectory. Of course the developers could try and catch all those things, but they rather spend their time thinking of new things :p Cheers, Tsjerk On Thu, Sep 27, 2012 at 2:18 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Sorry, but i was wrong, the .trr file contains trajectories and the .gro output file contains velocities as it should. Stelios On 09/27/2012 03:03 PM, Stelios Karozis wrote: Hi Tsjerk, I checked my .trr file and it contains the velocities, as it should. Stelios On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul jalem...@vt.edu έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the p... The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you wou... -- Justin A. Lemkul, Ph.D. Research Scientist Department ... -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- 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] doubt in minimization part
On 9/28/12 4:25 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now I am confusing with the following ( shown at botom) part of the tutorial.Here minimization means to minimize system_inflated.gro, is it right? Then without .epr and .top files of system_inflated.gro how can I do this? You should have a topology of the system, and .mdp files are provided so you can assemble a .tpr file and run minimization. Individual commands are not provided at this point in the tutorial, because (as stated at the beginning of the tutorial) it is expected that the user is familiar with a basic Gromacs workflow, how to execute grompp and mdrun, etc. Subsequent minimization steps are performed on system_shrink*.gro files in the same manner. -Justin perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat -- Justin A. Lemkul, Ph.D. Research Scientist 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] tau_t and tc_grps for v-rescale (2)
On 9/28/12 3:18 AM, Felipe Pineda, PhD wrote: Hi again, I posted yesterday the query below, but have not received any feedback up to now. I would like to put my question in another way: in Justin's CAP-15 in DPPC tutorial he uses during NVT equilibration Bussi's thermostat (V-rescale) together with three separate coupling groups: ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein DPPC SOL_CL ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K), Is this separate coupling needed at all taking into account that this temperature coupling method produces the correct coupling? Is it probably better to use a single coupling constant (system) and so avoid problems using this artificial correction to deal with the hot solvent / cold solute artifact? Technically the correct way to do it is to use one global thermostat rather than individual ones, but multiple thermostats are used for the reason described. I think it is actually more to do with electrostatics approximations than the thermostat itself (i.e. plain cutoffs leading to poor energy conservation and thus heating of the solvent, which diffuses rapidly) than anything else, so using PME is more robust. Someone please correct me if I'm remembering wrong. I don't recall having seen a test of an inhomogeneous system with a single thermostat, so multiple thermostats remain common practice. There are numerous, extensive discussions in the list archive about these topics so I would encourage you to search around a bit. Could somebody kindly tell me how large could the coupling constant, tau_t, be? Is it OK to switch, e.g., from 0.1 to 0.3 ps after T equilibration is reached, i.e., during the production phase? This issue is discussed in the reference for the V-rescale thermostat (Bussi et al). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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: distance restraint
On 9/27/12 7:07 PM, pauladelgado wrote: *file alfadrest.itp* [ distance_restraints ] ; i j ? label funct loup1up2 weight 8002 10641 1 0 10.40.50.6 1 8040 10616 1 0 10.40.50.6 1 8067 10582 1 0 10.40.50.6 1 8104 10554 1 0 10.40.50.6 1 8283 10698 1 0 10.40.50.6 1 8259 10723 1 0 10.40.50.6 1 8222 10764 1 0 10.40.50.6 1 8189 10794 1 0 10.40.50.6 1 *file topol.top* ; Include Distance restraint file #ifdef DISRES #include alfadrest.itp #endif ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include gromos43a1.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 All of this appears normal. What about the question I posed before regarding an energy contribution from the restraints? Do you see it in the .log or .edr files? What is its magnitude? *file .mdp* ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run define = -DDISRES ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50; Maximum number of (minimization) steps to perform energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) ;Parametros distance restraint disre = simple; simple (per-molecule) distance restraints disre_fc= 1000 ; Force constant for distance restraints *Questions* 1.When I am doing the minimization it comes out this message: /Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 349 steps, but did not reach the requested Fmax 10. / What this implies, can i continue besides this message?Or it is better to do something about it? http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision 2.Can you recomend considerable literature on vacuum simulation? A simple Google search turns up lots. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] something wrong with BlueGene/P
Hi Kai, A system that is marginally stable frequently succeeds in propagating on one machine and fails on another. I've observed this even between Xeon and Opteron systems, which is fairly minor architectural difference. Since your system works in NVT but not NPT, this would seem to imply that the high pressure conditions are at fault. You may not be able to get away with a 2 fs timestep here. Try 1 fs or even 0.5 fs and see what happens. Cheers, MZ On Wed, Sep 26, 2012 at 7:51 AM, Bao Kai paeanb...@gmail.com wrote: Hi, all, I did many simulations with Gromacs on CO2 Water mixtures on my workstation with 8 cores in parallel, the results are pretty good. For bigger simulations, I turned to the BlueGene machine. The problem is that with exactly the same configuration files and same number of MPI tasks( 8 here) , I always got the following problems. 1773 1774 step 6870: Water molecule starting at atom 1375 can not be settled. 1775 Check for bad contacts and/or reduce the timestep if appropriate. 1776 Wrote pdb files with previous and current coordinates 1777 1778 Step 6871, time 6.871 (ps) LINCS WARNING 1779 relative constraint deviation after LINCS: 1780 rms 0.139809, max 0.559153 (between atoms 10 and 11) 1781 bonds that rotated more than 30 degrees: 1782 atom 1 atom 2 angle previous, current, constraint length 1783 10 11 78.50.1210 0.1813 0.1163 1784 10 12 90.00.1523 0.1152 0.1163 1785 1786 step 6871: Water molecule starting at atom 4576 can not be settled. 1787 Check for bad contacts and/or reduce the timestep if appropriate. 1788 1789 step 6871: Water molecule starting at atom 5794 can not be settled. 1790 Check for bad contacts and/or reduce the timestep if appropriate. 1791 Wrote pdb files with previous and current coordinates 1792 Wrote pdb files with previous and current coordinates 1793 1794 --- 1795 Program mdrun_bgp_d, VERSION 4.5.5 1796 Source code file: pme.c, line: 538 1797 1798 Fatal error: 1799 3 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. 1800 This usually means that your system is not well equilibrated. 1801 For more information and tips for troubleshooting, please check the GROMACS 1802 website at http://www.gromacs.org/Documentation/Errors When I do the energy minimization or the NVT equilibration, Gromacs worked pretty well. The problem happened when I turned to the NPT equilibration. The pressure and temperature were set to be 100bar and 318K respectively. When during the NPT equlibration, the temperature and pressure keep increasing before the program halt. 1161 1162 DD step 6499 load imb.: force 6.9% 1163 1164Step Time Lambda 116565006.50.0 1166 1167Energies (kJ/mol) 1168 AngleLJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1169 4.50025e+012.21540e+04 -7.02187e+02 -1.23033e+05 -1.27743e+04 1170 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) 1171-1.14310e+051.50736e+04 -9.92368e+043.74677e+02 -3.36430e+02 1172 Pressure (bar) Constr. rmsd 1173 1.53825e+031.53151e-06 1174 1175 DD step 6599 load imb.: force 5.1% 1176 1177Step Time Lambda 117866006.60.0 1179 1180Energies (kJ/mol) 1181 AngleLJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1182 5.41207e+012.32123e+04 -7.01221e+02 -1.23852e+05 -1.27349e+04 1183 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) 1184-1.14022e+051.50532e+04 -9.89688e+043.82147e+02 -3.35505e+02 1185 Pressure (bar) Constr. rmsd 1186 2.37940e+031.40409e-06 1187 1188 DD step 6699 load imb.: force 4.8% 1189 1190Step Time Lambda 119167006.70.0 1192 1193Energies (kJ/mol) 1194 AngleLJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1195 4.70219e+012.37867e+04 -6.99910e+02 -1.24021e+05 -1.26862e+04 1196 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) 1197-1.13574e+051.54884e+04 -9.80852e+044.03537e+02 -3.34252e+02 1198 Pressure (bar) Constr. rmsd 1199 3.01172e+031.56366e-06 1200 1201 DD step 6799 load imb.: force 6.7% 1202 1203Step Time Lambda 120468006.80.0 1205 1206Energies (kJ/mol) 1207
[gmx-users] g_hbond
Hi I have an alcohol system and I want to calculate the number of H bonds during the trajectory. My atom type labels are C2-C2-C2-CO-OH-HO. CO denotes carbon bonded to oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen. In g_hbond how do I specify my groups to consider for H bonding. If I uses group 0 which is the whole system it says that I have twice as many acceptors as donors, which shouldn't be the case. Cheers Gavin -- 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] g_hbond
On 9/28/12 8:53 AM, Gavin Melaugh wrote: Hi I have an alcohol system and I want to calculate the number of H bonds during the trajectory. My atom type labels are C2-C2-C2-CO-OH-HO. CO denotes carbon bonded to oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen. In g_hbond how do I specify my groups to consider for H bonding. If I uses group 0 which is the whole system it says that I have twice as many acceptors as donors, which shouldn't be the case. g_hbond uses atom names (not types) to determine what is considered a donor, acceptor, or H atom. If there is a problem with the number of acceptors or donors, then there is a problem with the way the atoms are named. Without seeing the [atoms] section of the topology or relevant snippet of the coordinate file, it's hard to say what's going on at this point. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Umbrella sampling-protein-ligand complex
On 9/28/12 9:27 AM, Archana Sonawani wrote: Hi, I have performed simulations for 3 different ligands complexed with the same protein. I want to compare the binding energies of these different three complexes. Will umbrella sampling be useful in this case? Several methods could be used, and umbrella sampling is certainly one of them. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] provide opt way to perform simulation for protein and peptide -reg
On 9/28/12 10:07 AM, venkatesh s wrote: Respected gromacs Users, i want perform stimulation for protein + peptide (in water medium only not membrane protein) 1. Can i use the Docked conformation (better conformation both protein + peptide make it as one file .pdb ) for perform simulation Yes. 2. Other than that manually edit the coordinate file after TER or END insert peptide amino acid (my peptide having a 5 amino acid ) I don't understand what you want to do here. pdb2gmx can deal with multiple proteins in a single coordinate file, with topologies written for each depending on what you choose for the -chainsep option. Different chain identifiers or TER delimiters can be used to indicate that a new molecule has started. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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: distance restraint
The distance restraint energy is arrond 13700 KJ/mol, is that ok?, but whta happend with mi resulting pdb, i can't appreciate the distance restraint s i made. With respect to vacuum simulation, i am doing energy minimization and md with no periodic boundaries, with coulombtype=Cutt-off and the cut-offs turn off (equal to 0), and the md with no pressure and temperature cuopling, is that ok? Also i am not going to do NVT and NPT because for what i understand this is to equilibrate solvent and ions and make sure that this surround the protein. -- View this message in context: http://gromacs.5086.n6.nabble.com/distance-restraint-tp5001387p5001407.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] Re: distance restraint
On 9/28/12 12:18 PM, pauladelgado wrote: The distance restraint energy is arrond 13700 KJ/mol, is that ok?, but whta happend with mi resulting pdb, i can't appreciate the distance restraint s i made. No, that's not OK. The very large value of energy suggests that the desired distances are not being achieved (which you can measure with g_dist). How close are the initial distances to the restraints you have set in the topology? With respect to vacuum simulation, i am doing energy minimization and md with no periodic boundaries, with coulombtype=Cutt-off and the cut-offs turn off (equal to 0), and the md with no pressure and temperature cuopling, is that ok? Also i am not going to do NVT and NPT because for what i understand this is to equilibrate solvent and ions and make sure that this surround the protein. The purpose of any ensemble is to obtain a conformational ensemble under those conditions. What it sounds like you're trying to do is run an NVE simulation, which can be very difficult to obtain. See the notes on the wiki for methodological issues. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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: distance restraint
Other thing is that i couldn't found a lot of literature about the conditions for vacuum simulations, can you help me with this please, Thanks a lot Justin Paula Here is the graph of energy of distance restraint http://gromacs.5086.n6.nabble.com/file/n5001409/Screenshot-1.png -- View this message in context: http://gromacs.5086.n6.nabble.com/distance-restraint-tp5001387p5001409.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] Re: distance restraint
On 9/28/12 12:25 PM, pauladelgado wrote: Other thing is that i couldn't found a lot of literature about the conditions for vacuum simulations, can you help me with this please, Thanks a lot Justin Searching Google Scholar for protein vacuum simulations (without quotes) turns up 38000 results. Surely something in there will be of use. Scientific database software will probably return even more pertinent results. Paula Here is the graph of energy of distance restraint http://gromacs.5086.n6.nabble.com/file/n5001409/Screenshot-1.png This doesn't answer the question I posed before. Please measure distances between the restrained atoms and compare with the restraints you're trying to impose. The initial geometry may not be amenable to such restraints. The magnitude of the energy suggests that your restraints are severely violated. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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: distance restraint
Yes i found this document Computer simulations: Orientation of Lysozyme in vacuum under the influence of an electric field where i found about the conditions i mentioned before for vacuum simulations. So what should i do? -- View this message in context: http://gromacs.5086.n6.nabble.com/distance-restraint-tp5001387p5001411.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] Re: distance restraint
On 9/28/12 12:53 PM, pauladelgado wrote: Yes i found this document Computer simulations: Orientation of Lysozyme in vacuum under the influence of an electric field where i found about the conditions i mentioned before for vacuum simulations. So what should i do? You've been asking about implementation of distance restraints. I don't know why you're using them and you won't answer the questions I'm asking. I'm afraid I am not prepared to try to guess at the solution to your problems or design your research when I know nothing about what you're trying to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] something wrong with BlueGene/P
Hi Kai, I would suggest running (Berendsen) NpT equilibration with a large tau_p, followed by a few cycles in which you lower tau_p. Hope it helps, Tsjerk On Sep 28, 2012 2:53 PM, Matthew Zwier mczw...@gmail.com wrote: Hi Kai, A system that is marginally stable frequently succeeds in propagating on one machine and fails on another. I've observed this even between Xeon and Opteron systems, which is fairly minor architectural difference. Since your system works in NVT but not NPT, this would seem to imply that the high pressure conditions are at fault. You may not be able to get away with a 2 fs timestep here. Try 1 fs or even 0.5 fs and see what happens. Cheers, MZ On Wed, Sep 26, 2012 at 7:51 AM, Bao Kai paeanb...@gmail.com wrote: Hi, all, I did many sim... -- 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:provide opt way to perform simulation for protein and peptide -reg
On 9/28/12 1:03 PM, venkatesh s wrote: Respected gromacs Users, I want perform protein (only one chain) + peptide (five amino acid) simulation to understand interaction between both (can say what role are playing peptide with protein ) so i did like this pdb2gmx -f prot.pdb -o pro.gro -water tip3p -ignh -chainsep ter but in my .top file [ molecules ] ; Compound#mols Protein_chain_A 1 Question 1. its shows only one chain actually want show 2 chains, but why it shows 1 chain ? The result implies that the two chains are not properly separated by a TER line. and may i want know above mentioned way of doing protein+ peptide molecular dynamics is correct? What you're doing is generating a topology; you're not running MD yet. The command line is syntactically correct, but there is something wrong with the input .pdb file, otherwise you would have two chains written to the topology. 2. other than that what else method or way is there perform protein peptide MDS kindly let me know? This question doesn't make sense to me. Running MD on a complex is certainly a viable way to study the interactions, but you're not even close to doing that yet since your topology is not yet correct. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Umbrella sampling-protein-ligand complex
Dear Justin, So do I have to carry out umbrella sampling simulations separately for the three complexes or put the three ligands together with the protein and pull the ligands one by one to calculate the binding energy. I am confused. Thanks in advance. Regards, Archana On Fri, Sep 28, 2012 at 8:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/28/12 9:27 AM, Archana Sonawani wrote: Hi, I have performed simulations for 3 different ligands complexed with the same protein. I want to compare the binding energies of these different three complexes. Will umbrella sampling be useful in this case? Several methods could be used, and umbrella sampling is certainly one of them. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Archana Sonawani-Jagtap Junior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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-protein-ligand complex
On 9/28/12 2:19 PM, Archana Sonawani wrote: Dear Justin, So do I have to carry out umbrella sampling simulations separately for the three complexes or put the three ligands together with the protein and pull the ligands one by one to calculate the binding energy. I am confused. Each complex has to be treated separately. Simultaneously pulling three molecules won't make any physical sense and the simulations would crash anyway. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] mails of other users in this mailing list
Hello Is there a way to get all mails from the GROMACS mailing list for a special email adress? To be more precisely I want to have all messages that are asked and answered for a special user. This is motivated out of the fact that I saw that I am not alone with my system. There are other people how wants to make md with very similar molecules and I want to read their questions and answers they got. Thanks for help Greetings Lara -- 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] mails of other users in this mailing list
On 9/28/12 3:07 PM, Lara Bunte wrote: Hello Is there a way to get all mails from the GROMACS mailing list for a special email adress? To be more precisely I want to have all messages that are asked and answered for a special user. This is motivated out of the fact that I saw that I am not alone with my system. There are other people how wants to make md with very similar molecules and I want to read their questions and answers they got. http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List currently displays a mirror of the Nabble site (http://gromacs.5086.n6.nabble.com/), and if you find a thread that this person has posted to, you should be able to click his/her name and see their posts, i.e. for me: http://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=user_nodesuser=225787 -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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: distance restraint
http://gromacs.5086.n6.nabble.com/file/n5001418/Screenshot-2.png This is the distance of one pair of atoms that i restraint. I apologize if i did't mention why i am using distance restraint, i am working with a protein obtained using homology modelling, the next step after i get the protein structure is doing molecular docking, the problem is that i need to refine the structure and i found in literature that the protein goes through a conformational change where it forms a bundle of 4 alfa helix (hydrofobic interactions) before it interacts with its ligand, so besides of making the refinment of the structure i need to obtain that bundle in order to do molecular docking. The reason for doing the refinement in vacuo is that when you minimize a struture to avoid steric clashes i always make them in vacuo with other software, the problem is that i need to form the bundle and the software i usually used doesn't handle position restraint. My intention never was to bother you, I am very thankful for your time to answer my questions. Sorry for all the inconvenience Paula -- View this message in context: http://gromacs.5086.n6.nabble.com/distance-restraint-tp5001387p5001418.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] Re: distance restraint
On 9/28/12 3:34 PM, pauladelgado wrote: http://gromacs.5086.n6.nabble.com/file/n5001418/Screenshot-2.png This is the distance of one pair of atoms that i restraint. I apologize if i did't mention why i am using distance restraint, i am working with a protein obtained using homology modelling, the next step after i get the protein structure is doing molecular docking, the problem is that i need to refine the structure and i found in literature that the protein goes through a conformational change where it forms a bundle of 4 alfa helix (hydrofobic interactions) before it interacts with its ligand, so besides of making the refinment of the structure i need to obtain that bundle in order to do molecular docking. The reason for doing the refinement in vacuo is that when you minimize a struture to avoid steric clashes i always make them in vacuo with other software, the problem is that i need to form the bundle and the software i usually used doesn't handle position restraint. My intention never was to bother you, I am very thankful for your time to answer my questions. The distance shown is constant at roughly 8 nm. Your topology specifies that the desired restraints (though there are multiple, so are we to assume that all of the distances are similar?) are in the ballpark of 0.5 nm. The use of distance restraints is not to severely modify a structure. Instead of doing this, the algorithm will fail, as you are seeing, resulting in very large energies. I don't know if this is a viable route for the refinement you seek - if very large structural changes are expected, then extensive MD simulation will be required. Conformational changes can occur spontaneously or can be induced with steered MD (pull code), though care needs to be taken with the latter approach, as undesired structural changes can certainly occur if done incorrectly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Notes and warnings using grompp
Hi, I´m getting the following notes when using grompp to generate the tpr file. My system is a protein in water. I already checked the topology file and the sum of my charges are -13. Should I ignore it? Why is it assuming that value? NOTE 1 [file OmpC.top, line 23461]: System has non-zero total charge: -13.02 Total charge should normally be an integer. The second note is the following. Largest charge group radii for Van der Waals: 0.250, 0.244 nm Largest charge group radii for Coulomb: 0.084, 0.084 nm NOTE 2 [file min0.0.mdp]: The sum of the two largest charge group radii (0.494582) is larger than rlist (1.00) - rvdw (0.90) Thank you in advance, Sonia Aguilera Graduate student-Chemical Engineering Department Universidad de los Andes 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
Re: [gmx-users] Notes and warnings using grompp
On 9/28/12 4:10 PM, Sonia Milena Aguilera Segura wrote: Hi, I´m getting the following notes when using grompp to generate the tpr file. My system is a protein in water. I already checked the topology file and the sum of my charges are -13. Should I ignore it? Why is it assuming that value? NOTE 1 [file OmpC.top, line 23461]: System has non-zero total charge: -13.02 Total charge should normally be an integer. You need to add counterions. Please consult basic tutorial material. The second note is the following. Largest charge group radii for Van der Waals: 0.250, 0.244 nm Largest charge group radii for Coulomb: 0.084, 0.084 nm NOTE 2 [file min0.0.mdp]: The sum of the two largest charge group radii (0.494582) is larger than rlist (1.00) - rvdw (0.90) http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Notes and warnings using grompp
Hi, I´m getting the following notes when using grompp to generate the tpr file. My system is a protein in water. I already checked the topology file and the sum of my charges are -13. Should I ignore it? Why is it assuming that value? NOTE 1 [file OmpC.top, line 23461]: System has non-zero total charge: -13.02 Total charge should normally be an integer. The second note is the following. Largest charge group radii for Van der Waals: 0.250, 0.244 nm Largest charge group radii for Coulomb: 0.084, 0.084 nm NOTE 2 [file min0.0.mdp]: The sum of the two largest charge group radii (0.494582) is larger than rlist (1.00) - rvdw (0.90) Thank you in advance, Sonia Aguilera Graduate student-Chemical Engineering Department Universidad de los Andes 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] Re: Notes and warnings using grompp
Hi, I understand that usually it is needed to add counterions . I´m performing a free energy calculation and I want to see the free energy change without adding the ions. What I´m asking is why the program reads a total charge of -13.02 not 13.0. The note says that it must be an integer, but I don´t know what to change or where. Should I ignore the note? I have seen (second note) that since it is just a note, it can be ignored, but according with the parameters of the note, what do you think? Thank you, Sonia Aguilera -- View this message in context: http://gromacs.5086.n6.nabble.com/Notes-and-warnings-using-grompp-tp5001422p5001426.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] Re: Notes and warnings using grompp
On 9/28/12 5:13 PM, Sonia Aguilera wrote: Hi, I understand that usually it is needed to add counterions . I´m performing a free energy calculation and I want to see the free energy change without adding the ions. What I´m asking is why the program reads a total charge of -13.02 not 13.0. The note says that it must be an integer, but I don´t know what to change or where. Should I ignore the note? grompp reads a net charge of -13 because that's the charge (almost certainly) on the protein, per the parameters in the topology. -13.02 is close enough to an integer that the minor difference is due to rounding, as the link I provided before states. Whether or not you ignore it depends on whether or not you think whatever you are modeling is reasonable. I have seen (second note) that since it is just a note, it can be ignored, but according with the parameters of the note, what do you think? Notes are there to warn you that something is potentially wrong. It looks like either your .mdp settings are inappropriate or you have a large charge group. This situation can lead to artifacts from incorrect neighbor searching or nonbonded calculations. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
