[gmx-users] Re: mdrun -rerun and box size bug not fixed?
Hi, Thanks David, it helps when you know there is light at the end of the tunnel. Using PME didn't have any effect, but using a full precision trajectory reproduced energies up to 5e-3 kJ/mol. So the imprecision of the xtc coordinates causes the inaccuracy of the energies, i.e. creates a systematic bias towards high energies. This can actually be explained by the fact that bonded potential energy functions have a positive second derivative, as well as the Lennard Jones potential in the region which contributes most to the total energy. It is easy to see that a random and symmetric noise epsilon on the position x (truncation error in the xtc file) gives values of U(x+epsilon) whose average is larger than U(x) if U''(x) > 0. As far as I am concerned, I don't have the trr files anymore for my system. I can forget about accurate energies... But it's good to know that the effect exists, and can lead to biases of the order 2.5% on bonded energies with the xtc precision. Bye, Michel So I guess what I'm saying is that in principle you should be able to get good energies with rerun. Maybe you should try and narrow down the problem by doing some testing: (a) Do some reprocessing with PME rather than RF to see if that helps. (b) Do some reprocessing on full precision trajectories rather than xtcs to rule out precision issues etc. Best wishes, David == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: mdrun -rerun and box size bug not fixed?
Hi, > By reactivating the barostat as mentioned below, I managed to recover LJ > energies within 0.1% for my test system, which was a box of 1136 waters. > So I applied the same thing to my system of interest (a 605 residue > protein with around 25000 waters). The only difference is that the run > was done with PME, and the rerun is done with RF, so I cannot compare > electrostatics. For the other energies I get a systematic bias with > respect to the original run, for example : > >- LJ : 70 +-50 kJ/mol higher than original (0.05% of total) >- g96 bonds : 160 +-60 kJ/mol higher than original (2.44% of total) > > These biases are very reproducible over many trajectories with this > system. The LJ bias might be considered negligible as it is a small > percentage of the total LJ energy. However, the g96 bond bias is > surprising (bonds are present only in the protein). We expect that the > inaccuracy of the xtc coordinates generates some random noise. But I > don't understand how it could generate a systematic error of that > magnitude (2.44%) ... > > I tried to change different parameters to trace the origin of this bias > : version of gmx, platform, huge compressibility, turning off the > thermostats (for the g96 bond part), etc... Only turning the constraints > off influenced the results, yielding an even higher bias towards higher > g96 energies (210 +-60 kJ/mol). > > Have such inaccuracies been observed before with -rerun? Am I doing > something wrong or is there no hope of recovering better energies with a > rerun? We routinely do reprocessing with the *same* settings we run with (this is in the NVT ensemble, usually) and recover energies that are very close (i.e. what one would expect from the trajectory precision). Note this is using full precision trajectories, though. See for example http://dx.doi.org/10.1021/jp0735987. So I guess what I'm saying is that in principle you should be able to get good energies with rerun. Maybe you should try and narrow down the problem by doing some testing: (a) Do some reprocessing with PME rather than RF to see if that helps. (b) Do some reprocessing on full precision trajectories rather than xtcs to rule out precision issues etc. Best wishes, David > Thanks, > Michel > > > Original Message > Subject:Re: mdrun -rerun and box size bug not fixed? > Date: Tue, 06 Nov 2007 14:12:29 +0100 > From: Michel Cuendet <[EMAIL PROTECTED]> > To: gmx-users@gromacs.org > References: <[EMAIL PROTECTED]> > > Hi, > > I think I got it :-) Using gmx 3.3.1 with the same thermostat and > barostat settings as the original run, I get the right LJ energies > within 0.1%. I used tcoupl and pcoupl = "no" because I somehow > remembered that thermostats could do weird things when rerunning (see > the old thread : > http://www.gromacs.org/pipermail/gmx-developers/2005-August/001290.html ) > > But apparently the box is not reread form the trajectory if the pcoupl > option is deactivated. It would be much safer for users if the > appropriate options were automatically set when -rerun in invoked: > > nstlist = 1 > nstenergy = 1 > NO rescaling of velocities > NO rescaling of box size > Do read the box sizes from the trajectory > > Cheers, > > Michel > > > > == > Michel Cuendet, Ph.D > Molecular Modeling Group > Swiss Institute of Bioinformatics > CH-1015 Lausanne, Switzerland > www.isb-sib.ch/groups/Molecular_Modeling.htm > == > > > > > > > -- > > == > Michel Cuendet, Ph.D > Molecular Modeling Group > Swiss Institute of Bioinformatics > CH-1015 Lausanne, Switzerland > www.isb-sib.ch/groups/Molecular_Modeling.htm > == > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: mdrun -rerun and box size bug not fixed?
Dear all, By reactivating the barostat as mentioned below, I managed to recover LJ energies within 0.1% for my test system, which was a box of 1136 waters. So I applied the same thing to my system of interest (a 605 residue protein with around 25000 waters). The only difference is that the run was done with PME, and the rerun is done with RF, so I cannot compare electrostatics. For the other energies I get a systematic bias with respect to the original run, for example : - LJ : 70 +-50 kJ/mol higher than original (0.05% of total) - g96 bonds : 160 +-60 kJ/mol higher than original (2.44% of total) These biases are very reproducible over many trajectories with this system. The LJ bias might be considered negligible as it is a small percentage of the total LJ energy. However, the g96 bond bias is surprising (bonds are present only in the protein). We expect that the inaccuracy of the xtc coordinates generates some random noise. But I don't understand how it could generate a systematic error of that magnitude (2.44%) ... I tried to change different parameters to trace the origin of this bias : version of gmx, platform, huge compressibility, turning off the thermostats (for the g96 bond part), etc... Only turning the constraints off influenced the results, yielding an even higher bias towards higher g96 energies (210 +-60 kJ/mol). Have such inaccuracies been observed before with -rerun? Am I doing something wrong or is there no hope of recovering better energies with a rerun? Thanks, Michel Original Message Subject:Re: mdrun -rerun and box size bug not fixed? Date: Tue, 06 Nov 2007 14:12:29 +0100 From: Michel Cuendet <[EMAIL PROTECTED]> To: gmx-users@gromacs.org References: <[EMAIL PROTECTED]> Hi, I think I got it :-) Using gmx 3.3.1 with the same thermostat and barostat settings as the original run, I get the right LJ energies within 0.1%. I used tcoupl and pcoupl = "no" because I somehow remembered that thermostats could do weird things when rerunning (see the old thread : http://www.gromacs.org/pipermail/gmx-developers/2005-August/001290.html ) But apparently the box is not reread form the trajectory if the pcoupl option is deactivated. It would be much safer for users if the appropriate options were automatically set when -rerun in invoked: nstlist = 1 nstenergy = 1 NO rescaling of velocities NO rescaling of box size Do read the box sizes from the trajectory Cheers, Michel == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == -- == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Re: mdrun -rerun and box size bug not fixed?
From: Michel Cuendet <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Re: mdrun -rerun and box size bug not fixed? Date: Tue, 6 Nov 2007 15:26:54 +0100 Hi Berk, Thanks for your reply. The box is read, but in several parts of the code there are optimizations for fixed box dimensions (i.e. no pcoupl, no deform). This is indeed a bit tricky, but I don't know if we would want to change this for the rerun option. Maybe the optimizations are not necessary for the rerun option, as energy evaluations usually involve a limited number of frames. I think that the box sizes should really be read from the traj. The present behavior seems dangerous (I almost wasted a week of work figuring it out, and some users might never double check...) The optimizations are certainly not necessary, but currently the information that we are doing a rerun is not passed on to any routine except for the main loop. We would have to pass this information along. We do want scaling of velocties, since this influences the kinetic energy, also for reruns. I never understood this one. The kinetic energy at step N should depend only on the velocities at time step N. If a frame in the trajectory contains the positions and velocities at time step N as it should, no rescaling is necessary. If on the other hand only velocities at step N-1/2 are saved, velocities at step N+1/2 would have to be calculated in order to get accurate kinetic energy at step N. In this case, rescaling indeed needs to take place. But the rescaling will be nonsense if a Nosé- Hoover thermostat is used, since the thermostat momentum is not read from the trajectory. If this is the case, there should be a large warning sign when using -rerun with Nosé-Hoover. A solution would be to output the kinetic energy at time step N-1/2 during the rerun, which is in any case more accurate than the one at step N, and is just as good for statistics. Ekin[t] = (Ekin[t-dt/2]+Ekin[t+dt/2])/2 This currently indeed goes wrong with Nose-Hoover, since the current trajectory formats can not store the Nose-Hoover variables. The kinetic energy at half steps does not match the potential energy at the full step for calculating the total energy. In general we do not want anything different to happen during an rerun than would happen during a normal run, exactly to avoid discrepancies between normal runs and reruns. Therefore we would like to avoid passing along the rerun info deeping into the code. See a paper coming soon in JCP: M. M. A. Cuendet and W. F. van Gunsteren, On the calculation of velocity-dependent properties in molecular dynamics simulations using the leap-frog integration algorithm, J. Chem. Phys. (in print) (2007). We could consider using nstenergy=1 for rerun, but I think that currently you should already get the energy as often as for the original run, unless you use a trajectory without step numbers (e.g. pdb). This is good, but without nstenergy=1 the averages are wrong in md.log and at the end of the run. This is a nasty issue that we still have not fixed. We should fix this, but things are complicated due to the way the averages and fluctations are stored. Berk. _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: mdrun -rerun and box size bug not fixed?
Hi Berk, Thanks for your reply. The box is read, but in several parts of the code there are optimizations for fixed box dimensions (i.e. no pcoupl, no deform). This is indeed a bit tricky, but I don't know if we would want to change this for the rerun option. Maybe the optimizations are not necessary for the rerun option, as energy evaluations usually involve a limited number of frames. I think that the box sizes should really be read from the traj. The present behavior seems dangerous (I almost wasted a week of work figuring it out, and some users might never double check...) We do want scaling of velocties, since this influences the kinetic energy, also for reruns. I never understood this one. The kinetic energy at step N should depend only on the velocities at time step N. If a frame in the trajectory contains the positions and velocities at time step N as it should, no rescaling is necessary. If on the other hand only velocities at step N-1/2 are saved, velocities at step N+1/2 would have to be calculated in order to get accurate kinetic energy at step N. In this case, rescaling indeed needs to take place. But the rescaling will be nonsense if a Nosé- Hoover thermostat is used, since the thermostat momentum is not read from the trajectory. If this is the case, there should be a large warning sign when using -rerun with Nosé-Hoover. A solution would be to output the kinetic energy at time step N-1/2 during the rerun, which is in any case more accurate than the one at step N, and is just as good for statistics. See a paper coming soon in JCP: M. M. A. Cuendet and W. F. van Gunsteren, On the calculation of velocity-dependent properties in molecular dynamics simulations using the leap-frog integration algorithm, J. Chem. Phys. (in print) (2007). We could consider using nstenergy=1 for rerun, but I think that currently you should already get the energy as often as for the original run, unless you use a trajectory without step numbers (e.g. pdb). This is good, but without nstenergy=1 the averages are wrong in md.log and at the end of the run. Bye, Michel == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne Switzerland == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Re: mdrun -rerun and box size bug not fixed?
From: Michel Cuendet <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Re: mdrun -rerun and box size bug not fixed? Date: Tue, 06 Nov 2007 14:12:29 +0100 Hi, I think I got it :-) Using gmx 3.3.1 with the same thermostat and barostat settings as the original run, I get the right LJ energies within 0.1%. I used tcoupl and pcoupl = "no" because I somehow remembered that thermostats could do weird things when rerunning (see the old thread : http://www.gromacs.org/pipermail/gmx-developers/2005-August/001290.html ) But apparently the box is not reread form the trajectory if the pcoupl option is deactivated. It would be much safer for users if the appropriate options were automatically set when -rerun in invoked: nstlist = 1 nstenergy = 1 NO rescaling of velocities NO rescaling of box size Do read the box sizes from the trajectory Cheers, Michel The box is read, but in several parts of the code there are optimizations for fixed box dimensions (i.e. no pcoupl, no deform). This is indeed a bit tricky, but I don't know if we would want to change this for the rerun option. We do want scaling of velocties, since this influences the kinetic energy, also for reruns. Neighbor searching is already performed every step, independent of nstlist. We could consider using nstenergy=1 for rerun, but I think that currently you should already get the energy as often as for the original run, unless you use a trajectory without step numbers (e.g. pdb). Berk. _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: mdrun -rerun and box size bug not fixed?
Hi, I think I got it :-) Using gmx 3.3.1 with the same thermostat and barostat settings as the original run, I get the right LJ energies within 0.1%. I used tcoupl and pcoupl = "no" because I somehow remembered that thermostats could do weird things when rerunning (see the old thread : http://www.gromacs.org/pipermail/gmx-developers/2005-August/001290.html ) But apparently the box is not reread form the trajectory if the pcoupl option is deactivated. It would be much safer for users if the appropriate options were automatically set when -rerun in invoked: nstlist = 1 nstenergy = 1 NO rescaling of velocities NO rescaling of box size Do read the box sizes from the trajectory Cheers, Michel == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == LJ-rerun.eps Description: PostScript document ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: mdrun -rerun and box size bug not fixed?
Dear David and Berk, I have performed further tests on a box of 1136 waters with one sodium atom, to see if mdrun -rerun was able to reproduce the Lennard-Jones energies calculated during the run from frames stored in an xtc trajectory. I used three .gro files with grompp : - confin.gro, corresponds to step 0 - smallbox.gro, smaller box size - bigbox.gro, very large box size I checked the behavior of gromacs 3.3.0 with the bug fix provided in bugzilla (3.3.0_patch) and gromacs 3.3.1. Here are my observations: 1) Neither 3.3.0_patch nor 3.3.1 reproduce the LJ energies of the run. 2) 3.3.0_patch gives results that are independent of the .gro file. 3) 3.3.1 results depend on the .gro file. A small box makes energies explode. 4) 3.3.1 with a .gro corresponding to the initial condition gives the same results as 3.3.0_patch. 5) 3.3.1 with a very large box (no interaction between images ?) gives a good correlation with the run. I attach an eps figure illustrating the points above. The deviations between 3.3.0_patch and the energies from the run are about 8% of the total value, which can not be explained by the imprecisions of the positions in the .xtc file. Below is the .mdp file that I used for the run. For the rerun, I changed nstlist and nstenergy to 1. I also set tcoupl and pcoupl to "no". Tell me what you think about this. I am puzzled, especially about the behavior of 3.3.1 with confin.gro . Also point (5) above hints to the fact that LJ interactions between images are handeled wrongly by both 3.3.0_patch and 3.3.1. Cheers, Michel title= Na cpp = /lib/cpp include = -I../top integrator = md dt = 0.001 nsteps = 10 comm_mode = Linear nstcomm = 1 comm_grps = System nstxout = 1 nstvout = 0 nstlog = 1000 nstenergy= 1000 nstxtcout= 1000 xtc-grps = System nstlist = 5 ns_type = grid rlist= 0.8 coulombtype = reaction-field rcoulomb = 1.4 epsilon_rf = 80 vdw-type = cut-off rvdw = 1.4 tcoupl = nose-hoover tc-grps = System tau_t= 0.15 ref_t= 300 Pcoupl = parrinello-rahman tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no gen_temp = 300 gen_seed = 173529 Dear David and Berk, I am investigating further to understand why I don't get the same energies with -rerun. I will report next week. Thanks for your replies, Michel I just checked the 3.3.1 source code in md.c and the box is copied from the xtc file. I don't know where your problems could come from. Berk. From: "David Mobley" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] mdrun -rerun and box size bug not fixed? Date: Thu, 1 Nov 2007 06:12:56 -0700 Dear Michel, Are you sure you're using 3.3.1? I have not checked this specific issue -- but I have checked that if I run hydration free energy calculations in patched 3.3.0, and again in patched 3.3.1, and do my usual free energy analysis using mdrun -rerun, I get the same values. That either tells me that (a) the patch is in 3.3.1 also, or possibly (b) that the problem is small enough for hydration free energies that I'm missing it. Anyway, hopefully (a) is true, otherwise I'm going to need to repeat a LOT of work (and be very grumpy). Keep me posted on this. Thanks, David -- == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == LJ-rerun.eps Description: PostScript document ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: mdrun -rerun and box size bug not fixed?
Michel Cuendet wrote: Dear David and Berk, I am investigating further to understand why I don't get the same energies with -rerun. I will report next week. if you are using xtc files you will never get the same energies as in the original run because of the reduced precision in these files. Thanks for your replies, Michel I just checked the 3.3.1 source code in md.c and the box is copied from the xtc file. I don't know where your problems could come from. Berk. From: "David Mobley" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] mdrun -rerun and box size bug not fixed? Date: Thu, 1 Nov 2007 06:12:56 -0700 Dear Michel, Are you sure you're using 3.3.1? I have not checked this specific issue -- but I have checked that if I run hydration free energy calculations in patched 3.3.0, and again in patched 3.3.1, and do my usual free energy analysis using mdrun -rerun, I get the same values. That either tells me that (a) the patch is in 3.3.1 also, or possibly (b) that the problem is small enough for hydration free energies that I'm missing it. Anyway, hopefully (a) is true, otherwise I'm going to need to repeat a LOT of work (and be very grumpy). Keep me posted on this. Thanks, David == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: mdrun -rerun and box size bug not fixed?
Dear David and Berk, I am investigating further to understand why I don't get the same energies with -rerun. I will report next week. Thanks for your replies, Michel I just checked the 3.3.1 source code in md.c and the box is copied from the xtc file. I don't know where your problems could come from. Berk. From: "David Mobley" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] mdrun -rerun and box size bug not fixed? Date: Thu, 1 Nov 2007 06:12:56 -0700 Dear Michel, Are you sure you're using 3.3.1? I have not checked this specific issue -- but I have checked that if I run hydration free energy calculations in patched 3.3.0, and again in patched 3.3.1, and do my usual free energy analysis using mdrun -rerun, I get the same values. That either tells me that (a) the patch is in 3.3.1 also, or possibly (b) that the problem is small enough for hydration free energies that I'm missing it. Anyway, hopefully (a) is true, otherwise I'm going to need to repeat a LOT of work (and be very grumpy). Keep me posted on this. Thanks, David == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
