Re: [gmx-users] temperature shooting up
Dear Mark,Thanks for your help. Actually I did separate runs for flexible and rigid models, and didn't use the equilibrated flexible structure to start with rigid model calculations. But the starting configurations are the same. So do you mean I need to reduce the T-coupling time? If the initial water geometry is not the same as the rigid model, does the program will "enforce" that geometry for water molecules, or to "relax" water molecure towards it? Many thanks,CherryMark Abraham <[EMAIL PROTECTED]> wrote: Cherry Y. Yates wrote:> Dear Mark,> > Thanks for your help, I followed you instruction, and I can get stable > temperature after I remove the temperature coupling. In this case I used > the flexible spc itp file. However if I use a rigid spc.itp, after > remveing the temperature coupling, the system temperature is shooting up > from 300K to thousands degree, the total energy is going up also instead > of fluctuating. I attached both the itp files and grompp.mdp files. Let > me know what could be wrong. It is really wired to me.The change in the model physics from flexible to rigid is severe one - almost all of the water molecules won't fit the rigid geometry, and will thus be in a high-potential-energy state. If the constraint-enforcing algorithm conserves energy, then that potential energy has to be converted to kinetic energy. Then if the simulation lacks temperature coupling, it is at constant energy and the temperature will be necessarily high. Actually you say you observe rising energy - this is probably because your timestep is too large to conserve energy at this very high temperature (and thus atomic velocity).So the take-home lesson is not to do two perturbations of your model physics at one time. If you really want to start with a flexible water model with temperature regulation and end up with rigid water model at without temperature regulation, do the water transition with temperature coupling still on to give the energy somewhere to flow - to the external bath. I expect you'd need a short temperature coupling constant to make this work in practice. Once that's stable, *now* try taking off temperature coupling.This suggests the question, why you'd want to do this flexible-rigid transition in an equilibration? It would be simpler to start in the rigid domain, and to do energy minimization to correct any geometries before starting MD simulations.Mark___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 __Do You Yahoo!?Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Understanding the output of g_rmsf
Hi Keith, Reference frame and reference structure are references to the same reference. It is the structure supplied with -s, and possibly a subset of the atoms in there, specified by an index group. The RMSF is indeed the standard deviation of the atomic displacement. That is an atom or residue based property defined over a certain time, which is recorded in the file specified with -o. The RMSD (-od [rmsdev.xvg]) is a structure based property, defined over a range of atoms per time, which is recorded for each frame in the trajectory. Thso the -o file is indexed per atom (or per residue with -res) and the -od file is indexed per time. Hence the differences between the numbers of entries. That has nothing to do with the reference. Best, Tsjerk On 11/8/06, Keith Ball <[EMAIL PROTECTED]> wrote: Hi, I have been a bit confused by the g_rmsf output. In the manual, it says that "g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after first fitting to a reference frame." But what *is* the reference frame? I assume that this output is what goes to the file specified by –o (rmsf.xvg, by default). The –od option (which goes to rmsdev.xvg by default) is the rms deviation "with respect to the reference structure". What reference structure? Is that the same as the "reference frame" mentioned above? I notice that the numbers in rmsf.svg and rmsdev.xvg are always different, so I assume not. Can anyone explain the difference between what goes into the –o file, and what goes into the –od file? Also, if I start at a specific frame (say, -b 1000, to start 1ns into the trajectory), is the conformation nearest t=1ns the reference frame/structure? Many thanks, Keith Keith D. Ball, PhD Staff Scientist Catalyst Biosciences 290 Utah Ave S. San Francisco, CA 94080 650-266-8661 (phone) 650-871-2475 (fax) [EMAIL PROTECTED] http://www.catbio.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Tsjerk A. Wassenaar, Ph.D. post-doc NMR, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] question about energy fluctuation
Hi all,After running a MD of a system with about 17000 atoms, I calculated the potential and the total-energy:*Last frame read 1557952 time 1557.952Statistics over 1557953 steps [ 0. thru 1557.9520 ps ], 2 data setsEnergy Average RMSD Fluct. Drift Tot-Drift--- Potential -273047 626.559 611.258 -0.305998 -476.731Total-Energy -184656 839.662 828.307 -0.305999 -476.731* I found that the Fluct./Average is 0.45% (Total-Energy), 0.22%(Potential). In the simulation, the time step is 0.001ps, and I saved the energy every step. On the other hand, on page 98 of the book "Computer Simulation of Liquids" (M. P. Allen & D. J. Tildesley), it is said "For a simple Lennard-Jones system, fluctuation of order 1 part in 10^4 are generally considered to be acceptable." The ratio obtained from Gromacs are quite bigger. Therefore, I want to know if there are any standard for different system to check whether the system are accetable or not.PS: Another question: I found only when the energy data are divided by the number of the molecules, the obtained result are consistent with the date in some related papers. In Gromacs, the unit of energy is KJ/mol. If divided by the number of molecules, how to consider the unit? Thanks for any suggestions!Sincerely yours,Baofu Qiao, PhD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Strange problem with simple FEP (bug?)
Thanks, but that's indeed not the problem. I'm just doing a PR-run in state A. State B is not of interest in that case. Somehow GROMACS mixes things up internally, I guess. The bugzilla-entry has been placed. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ David Mobley wrote: Maik, I'm trying to do a simple FEP within a simple protein, which seems to make things simple...but as you may expect...it is anything else than that. What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA. Therefore the CZ is changed from the type of TYR to the type of PHE. The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a dummy (PHE). So this is very simple. We checked the tpr-dump and everything looks fine (except, maybe, we missed it). Now, in the position-restraint run (where state B should not be regarded by the system), the OH-proton moves on top of the OH-oxygen and the simulation crashes after a while. We then performed a FEP from TYR to TYR (so A- and B-state are the same) and the system runs. I am not an OPLS guy myself, and I don't know the details of your transformation, so I'll just tell you one possibility, and you'll have to decide whether it could apply in your situation. Sometimes, if you are disappearing a Lennard-Jones site that still has some amount of electrostatics, it can begin to interpenetrate with other atoms which either do not have Lennard-Jones interactions (hydrogens in some force fields) or which do (depending on the combination rule you use). Obviously, this is bad because (for example) protons can move on top of oxygens and cause blowing up. A classic example of this is, for example, if I am turning off the LJ on an oxygen site at the same time as turning off the charges on that oxygen. In many FF's, water hydrogens lack LJ interactions, so they can come and overlap with the oxygen I'm disappearing, which is still charged (at least to some degree) and cause a "fusion" type event. I don't know if that's what's going on for you, but you might think about it -- do you have any atoms that you're disappearing, and are there other atoms which the combination rules would allow to overlap with those? The way I get around this problem in my calculations is to always turn off electrostatics on any atom I'm disappearing prior to modifying the LJ parameters, so that I never have a charged atom which is being treated using the "soft-core" potentials that allow overlap. Not sure if that's your problem -- just a thought. David The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions? Gerrit and me think of a bug somewhere. Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 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 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] calculating energy for more than 256 index groups
Hi, i want to calculate an interaction energy matrix for more than 256 energy groups. First grompp only accept 255 groups so i changed in readir.c #define MAXPTR 510 #define NOGID 511 (from 254 and 255) After that grompp writes out an tpr file and mdrun works without problems, but than in the log file there are only interactions calculated for the first 256 energy groups. what do i have to change also or is this somewhere an hard limit? greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Creation of an index file with seperate lipid leaflets
Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Alan Dodd University of Bristol __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Creation of an index file with seperate lipid leaflets
On Wed, 8 Nov 2006, Alan Dodd wrote: > Has anyone already created a way to generate an index > file with the atoms from the two leaflets of a bilayer > listed seperately? I can't believe it hasn't already > been done, but can't find a direct description of a > solution. I'm attempting a modification to make_ndx, > (or perhaps something considerably less ambitious, > judging by the way it's going so far) to permit lipid > selection based on headgroup orientation, though I'd > quite like to save myself the effort. > Incidentally, splitres and splitat seem to be the > wrong way around, unless I'm misunderstanding them - > they do the opposite of what they say. From the > gromacs 3.3.1 source download I did on April of this > year. Reordering the lipids into leaflets in your starting coordinate file might be a good idea. If you anticipate lipid exchange between leaflets, then a more general tool like what you suggest would be helpful. Jay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Creation of an index file with seperate lipid leaflets
Wouldn't shuffle/sort undo all the good work? I did wonder if I should have labelled the lipids in different leaflets as different molecule types, or different chains, but it's a bit late now... --- Jay Mashl <[EMAIL PROTECTED]> wrote: > On Wed, 8 Nov 2006, Alan Dodd wrote: > > Has anyone already created a way to generate an > index > > file with the atoms from the two leaflets of a > bilayer > > listed seperately? I can't believe it hasn't > already > > been done, but can't find a direct description of > a > > solution. I'm attempting a modification to > make_ndx, > > (or perhaps something considerably less ambitious, > > judging by the way it's going so far) to permit > lipid > > selection based on headgroup orientation, though > I'd > > quite like to save myself the effort. > > Incidentally, splitres and splitat seem to be the > > wrong way around, unless I'm misunderstanding them > - > > they do the opposite of what they say. From the > > gromacs 3.3.1 source download I did on April of > this > > year. > > Reordering the lipids into leaflets in your starting > coordinate > file might be a good idea. If you anticipate lipid > exchange between leaflets, > then a more general tool like what you suggest would > be helpful. > > Jay > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > Sponsored Link Mortgage rates near 39yr lows. $420k for $1,399/mo. Calculate new payment! http://www.LowerMyBills.com/lre ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] NPH simulation, constant enthalpy?
Dear Gromacs users, I have been trying to run an NPH (constant pressure and enthalpy) simulation of a LJ fluid (as a first test) with GROMACS. From what I understand (from the GROMACS manual and references therein), one can do that by considering a Parrinello-Rahman pressure coupling (and no thermostat). However, when I compute the enthalpy a posteriori using g_energy, it is far from constant and actually fluctuates a lot. But from the Nosé & Klein paper (cited in the manual, in the section on pressure coupling) it seems that I really should have a constant enthalpy, except for small fluctuations (associated to the degrees of freedom of the barostat, I believe). So I'm probably missing something. If anyone has ever tried similar simulations with Gromacs, I'd very much like any input or advice you might have on what I might be doing wrong. Thanks a lot. Adrien. -- Adrien Leygue Department of Materials Science and Engineering School of Chemical Engineering National Technical University of Athens 9 Heroon Polytechniou Street Zografou Campus, Athens 157 80, GREECE Tel/Fax: +30210 772-3112 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] pdb2gmx and protein DNA complexes
Hi I am trying to simulate a protein DNA complex but I am stuck at the pdb2gmx stage as it gets stuck when it encounters a nucleotide.Program pdb2gmx, VERSION 3.3Source code file: resall.c, line: 438 Fatal error:Residue 'C' not found in residue topology databaseThe pdb segment is as follows:ATOM 1239 NZ LYS B 513 -24.159 16.372 -25.774 1.00 51.42 NATOM 1249 N1 C C 1 - 10.253 8.018 40.704 1.00 25.86 NHas anyone encountered this problem before?RegardsDebo-- -Debojyoti Dutta, PhD (USC) http://catarina.usc.edu/~ddutta- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Creation of an index file with seperate lipid leaflets
Alan Dodd a écrit : Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Alan Dodd University of Bristol Inflategro, written by D. Tieleman and available at: http://moose.bio.ucalgary.ca/index.php?page=Programs allows easily to discriminate between upper and lower leaflet. This is not the program's goal, but if i were to start something, i would definively start looking at his program (in perl). With minor modifications (mostly removing unuseful code for you and creating the output index file), i think you should get what you want. HTH Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Creation of an index file with seperate lipid leaflets
On Wed, Nov 08, 2006 at 10:09:28AM -0600, Jay Mashl wrote: > On Wed, 8 Nov 2006, Alan Dodd wrote: > > Has anyone already created a way to generate an index > > file with the atoms from the two leaflets of a bilayer > > listed seperately? I can't believe it hasn't already > > been done, but can't find a direct description of a > > solution. I'm attempting a modification to make_ndx, > > (or perhaps something considerably less ambitious, > > judging by the way it's going so far) to permit lipid > > selection based on headgroup orientation, though I'd > > quite like to save myself the effort. > > Incidentally, splitres and splitat seem to be the > > wrong way around, unless I'm misunderstanding them - > > they do the opposite of what they say. From the > > gromacs 3.3.1 source download I did on April of this > > year. > > Reordering the lipids into leaflets in your starting coordinate > file might be a good idea. If you anticipate lipid exchange between leaflets, > then a more general tool like what you suggest would be helpful. look at the z-coordinates of the phosphorus atoms and expand these into full residues. you probably don't have flip-flop, so this is a static group. you can do this using the gromacs libraries, but with some clever use of logical operations you can also write a script around make_ndx. if you're lazy, you can probably also do it using my program g_under (contact off-list, i still haven't made a distribution). nothing against choosing a single water molecule as 'Peptide' and a cylinder with dimensions 8x8x1 nm (assuming bilayer normal is in z-direction). here's the help of the program: g_under can do a number of things on a group of atoms that are located in a specific direction under an other group. Typically one will want to extract the lipid molecules that are directly under a peptide that is binding to a membrane. Two index groups are required; one describing the Peptide, and one describing the Membrane. Subsequently all Membrane atoms that have all of their coordinates (x, y and z) within a threshold value of any of the Peptide atoms' x, y or z coordinate, are defined as being *under* the Protein. The threshold value in each direction is supplied with -d. For every frame output is written to these files: -oa: all atom numbers of this group, starting at zero. -or: all unique residue numbers of this group, starting at one. Output after this is affected by the operators set with -res and -and. -res expands the found atoms to include full residues -and gives the possibility to cross the resulting group with an other index group using the AND operator. When -od is given, the distance between the centers of mass of the resulting group and an other group is calculated. The total distance and its x, y and z components are plotted. This other group can have its atoms that make part of the UNDER group excluded when -not is given. If -coord is supplied, also the individual centre-of-mass coordinates of the two groups are plotted. cheers, marc -- Marc F. Lensink http://www.biochem.oulu.fi/~lensink/ Centre for Structural Biology and Bioinformatics SCMBB Université Libre de Bruxelles [EMAIL PROTECTED] Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium tel: +32 2 650 5411 secr: +32 2 650 2013 fax: +32 2 650 5425 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Creation of an index file with seperate lipid leaflets
Wasted work would be bad ;) Rather than headgroup orientation, maybe try looking at atom distributions along the bilayer normal direction. Neutron scattering experiments show that for atom groups far from the bilayer midplane, the corresponding z-coordinates form two distinct distributions. So one way could be the following. Pick a headgroup atom and obtain its z-coordinate. Have make_ndx accept this value as input. Search the system by looping over lipids and ask whether that atom type has a z-coordinate within some amount around the input value. From this you know the membership of the leaflets. A more automatic way would be to have the program first discern the distribution and then reread the system to decide the leaflet membership. Jay On Wed, 8 Nov 2006, Alan Dodd wrote: > Wouldn't shuffle/sort undo all the good work? I did > wonder if I should have labelled the lipids in > different leaflets as different molecule types, or > different chains, but it's a bit late now... > > --- Jay Mashl <[EMAIL PROTECTED]> wrote: > > > On Wed, 8 Nov 2006, Alan Dodd wrote: > > > Has anyone already created a way to generate an > > index > > > file with the atoms from the two leaflets of a > > bilayer > > > listed seperately? I can't believe it hasn't > > already > > > been done, but can't find a direct description of > > a > > > solution. I'm attempting a modification to > > make_ndx, > > > (or perhaps something considerably less ambitious, > > > judging by the way it's going so far) to permit > > lipid > > > selection based on headgroup orientation, though > > I'd > > > quite like to save myself the effort. > > > Incidentally, splitres and splitat seem to be the > > > wrong way around, unless I'm misunderstanding them > > - > > > they do the opposite of what they say. From the > > > gromacs 3.3.1 source download I did on April of > > this > > > year. > > > > Reordering the lipids into leaflets in your starting > > coordinate > > file might be a good idea. If you anticipate lipid > > exchange between leaflets, > > then a more general tool like what you suggest would > > be helpful. > > > > Jay > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > 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 > > > > > > > > > Sponsored Link > > Mortgage rates near 39yr lows. $420k for $1,399/mo. > Calculate new payment! > http://www.LowerMyBills.com/lre > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > -- R. Jay Mashl University of Illinois [EMAIL PROTECTED] (Tel)217-244-5818 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] pdb2gmx and protein DNA complexes
Yes, very recently actually. What forcefield are you using? If you're using the AMBERXX-port, you might want to have a look at http://folding.stanford.edu/ffamber/. Regardless of your ff, make sure that the atoms in your pdb match the ones in ff[your_forcefield].rtp. Oh, and read the manual. /Erik - Original Message - From: Debojyoti Dutta To: gmx-users@gromacs.org Sent: Wednesday, November 08, 2006 6:08 PM Subject: [gmx-users] pdb2gmx and protein DNA complexes Hi I am trying to simulate a protein DNA complex but I am stuck at the pdb2gmx stage as it gets stuck when it encounters a nucleotide.Program pdb2gmx, VERSION 3.3Source code file: resall.c, line: 438 Fatal error:Residue 'C' not found in residue topology databaseThe pdb segment is as follows:ATOM 1239 NZ LYS B 513 -24.159 16.372 -25.774 1.00 51.42 NATOM 1249 N1 C C 1 - 10.253 8.018 40.704 1.00 25.86 NHas anyone encountered this problem before?RegardsDebo-- -Debojyoti Dutta, PhD (USC)http://catarina.usc.edu/~ddutta- ___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 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] pdb2gmx and protein DNA complexes
...and not just the atoms. Make sure that the residue names are the correct ones for your forcefield. Apparently, the forcefield you're using does not have a 'C'-residue. /Erik - Original Message - From: Erik Marklund To: Discussion list for GROMACS users Sent: Wednesday, November 08, 2006 6:44 PM Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes Yes, very recently actually. What forcefield are you using? If you're using the AMBERXX-port, you might want to have a look at http://folding.stanford.edu/ffamber/. Regardless of your ff, make sure that the atoms in your pdb match the ones in ff[your_forcefield].rtp. Oh, and read the manual. /Erik - Original Message - From: Debojyoti Dutta To: gmx-users@gromacs.org Sent: Wednesday, November 08, 2006 6:08 PM Subject: [gmx-users] pdb2gmx and protein DNA complexes Hi I am trying to simulate a protein DNA complex but I am stuck at the pdb2gmx stage as it gets stuck when it encounters a nucleotide.Program pdb2gmx, VERSION 3.3Source code file: resall.c, line: 438 Fatal error:Residue 'C' not found in residue topology databaseThe pdb segment is as follows:ATOM 1239 NZ LYS B 513 -24.159 16.372 -25.774 1.00 51.42 NATOM 1249 N1 C C 1 - 10.253 8.018 40.704 1.00 25.86 NHas anyone encountered this problem before?RegardsDebo-- -Debojyoti Dutta, PhD (USC)http://catarina.usc.edu/~ddutta- ___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 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] How to generate GRO and TOP file for high-number-atom polymer?
Hi, Genearlly I generate GRO and TOP file for polymer using PRODRG. But PRODRG does not work when the atom number of the polymer exceeds 300. So can anyone recommend other software and method? Thanks. Yours Sincerely, WU Yanbin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] What if the atom number exceed 99999 for Gromacs file?
Hi, I built up a box of polymer with box size 20x20x20 and then solvate the box with water using Genbox. Thus the total atom number exceeds 9 and I found that the atom number starts from zero when it exceeds 9. Does it matter for the ongoing command "grompp" and "mdrun"? Thanks. Yours Sincerely, WU Yanbin -- ---WU YanbinDepartment of Mechanical Science and EngineeringEmail: [EMAIL PROTECTED]3323 Beckman Institute Phone: (217)819-9064University of Illinois at Urbana-Champaign405 N. Mathews AvenueUrbana, IL 61801--- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] What if the atom number exceed 99999 for Gromacs file?
I believe, It does not matter. On 11/8/06, WU Yanbin <[EMAIL PROTECTED]> wrote: Hi, I built up a box of polymer with box size 20x20x20 and then solvate the box with water using Genbox. Thus the total atom number exceeds 9 and I found that the atom number starts from zero when it exceeds 9. Does it matter for the ongoing command "grompp" and "mdrun"? Thanks. Yours Sincerely, WU Yanbin -- ---WU YanbinDepartment of Mechanical Science and EngineeringEmail: [EMAIL PROTECTED]3323 Beckman Institute Phone: (217)819-9064University of Illinois at Urbana-Champaign 405 N. Mathews AvenueUrbana, IL 61801--- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Viswanadham Sridhara,Research Assistant,Old Dominion University,Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] temperature shooting up
Cherry Y. Yates wrote: Dear Mark, Thanks for your help. Actually I did separate runs for flexible and rigid models, and didn't use the equilibrated flexible structure to start with rigid model calculations. But the starting configurations are the same. Oh OK - but the same kind of problem can arise if your starting configuration doesn't match the constraints of the rigid model. So do you mean I need to reduce the T-coupling time? See section 3.4.5 of the manual. The smaller the T-coupling time, the "harder" the T-coupling constraint is. If the initial water geometry is not the same as the rigid model, does the program will "enforce" that geometry for water molecules, or to "relax" water molecure towards it? As I said last time, It would be simpler ... to do energy minimization to correct any geometries before starting MD simulations. I've never needed to do this, so can't help with details, but it may be necessary for this EM to use a solvent molecule .itp that has real bonded functions rather than constraints. Thus this EM is actually doing the geometry correction, and the geometry constraint algorithms for MD will work as you'd hope. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] question about energy fluctuation
Qiao Baofu wrote: Hi all, After running a MD of a system with about 17000 atoms, I calculated the potential and the total-energy: * Last frame read 1557952 time 1557.952 Statistics over 1557953 steps [ 0. thru 1557.9520 ps ], 2 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -273047626.559611.258 -0.305998 -476.731 Total-Energy-184656839.662828.307 -0.305999 -476.731 * I found that the Fluct./Average is 0.45% (Total-Energy), 0.22%(Potential). In the simulation, the time step is 0.001ps, and I saved the energy every step. On the other hand, on page 98 of the book "Computer Simulation of Liquids" (M. P. Allen & D. J. Tildesley), it is said "For a simple Lennard-Jones system, fluctuation of order 1 part in 10^4 are generally considered to be acceptable." This book was written nearly 20 years ago, so take with a "grain of salt" its advice on "general acceptability". Was this a simple Lennard-Jones system? If not, you are comparing apples and oranges anyway. The ratio obtained from Gromacs are quite bigger. Therefore, I want to know if there are any standard for different system to check whether the system are accetable or not. PS: Another question: I found only when the energy data are divided by the number of the molecules, the obtained result are consistent with the date in some related papers. In Gromacs, the unit of energy is KJ/mol. If divided by the number of molecules, how to consider the unit? kJ/mol per molecule? :-P The conversion is straightforward, but you may find it easier conceptually to convert your other sources into kJ/mol. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] invalid order of directive moleule type
Thanks for the valueable suggessions, but sir i am actually want to use this program for small molecules. I have taken single FAD molecule as u suggested modified the atom type as described in ffgmx.rtp, program results top and gro files using pdb2gmx, but while running grompp i am getting the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations WARNING 1 [file "fad.top", line 128]: No default Bond types, using zeroes WARNING 2 [file "fad.top", line 139]: No default Bond types, using zeroes WARNING 3 [file "fad.top", line 141]: No default Bond types, using zeroes WARNING 4 [file "fad.top", line 328]: No default Angle types, using zeroes WARNING 5 [file "fad.top", line 329]: No default Angle types, using zeroes WARNING 6 [file "fad.top", line 334]: No default Proper Dih. types, using zeroes WARNING 7 [file "fad.top", line 336]: No default Proper Dih. types, using zeroes WARNING 8 [file "fad.top", line 338]: No default Proper Dih. types, using zeroes WARNING 9 [file "fad.top", line 341]: No default Proper Dih. types, using zeroes WARNING 10 [file "fad.top", line 343]: No default Proper Dih. types, using zeroes Cleaning up temporary file gromppLLm3l8 --- Program grompp, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated --- "I Need Love, Not Games" (Iggy Pop & Kate Pierson) Moreover , suppose if we want to use this program (grompp) for say, a molecule which has no entry in any .rtp file provided with Gromacs and we use the PRODRG server, then how to deal with the error "invalid molecular directive type". Kindly explain me regarding this error in detail, if you can spare some time for me. If you want i can give the sample files for what i am trying to do. Thanks From: "merc mertens" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] invalid order of directive moleule type Date: Tue, 07 Nov 2006 13:00:02 +0100 if i were you, i would rather adapt my pdb file to an existing forcefield as ffgmx, than trying to generate a new forcefield that fits to your pdb with prodrug. the first option seems much easier to me. what i mean is, if you change the names of you FAD atoms to the ones you see in the *rtp they will be recognized by pdb2gmx. Original-Nachricht Datum: Tue, 07 Nov 2006 11:35:47 + Von: "harpreet singh" <[EMAIL PROTECTED]> An: gmx-users@gromacs.org Betreff: [gmx-users] invalid order of directive moleule type > Hi All, > I am new to this package and want your help. I am trying to use GROMACS to > study energy minimization and molecular dynamics for FAD molecule. I am > having the following problems. > 1. I tried to run pdb2gmx for PDB file for FAD downloaded from > http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl site. and used the > gromacs force field . The program gave the following error: - > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.hdb > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx-n.tdb > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx-c.tdb > > Back Off! I just backed up fad_test.top to ./#fad_test.top.1# > Processing chain 1 (53 atoms, 1 residues) > There are 0 donors and 0 acceptors > There are 0 hydrogen bonds > --- > Program pdb2gmx, VERSION 3.3.1 > Source code file: pdb2gmx.c, line: 393 > Fatal error: > Atom O1P in residue FAD 1 not found in rtp entry with 61 atoms > while sorting atoms > On comparing topology file (ffgmx.rtp) for FAD entry i was surpried to see > that it has atom type enteries OP1, OP2 instead of O1P, O2P in downloaded > PDB file (fad.pdb). Also atom type at number 23 was O in ffgmx.rtp (for > FAD) and O3P was missing in this file. I am attaching the files herewith. > > 2. I tried to make .top and .gro files (fad92.top and fad.gro > respectively) > ,using PRODRG2 server. and used them with grompp commad > > grompp -f em.mdp -c fad92.gro -p fad92.top -o fad92.tpr > > This resulted in the following error. > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# > checking input for internal consistency... > calling /usr/bin/cpp... > processing topology... > Cleaning up temporary file gromppfYcUxi > --- > Program grompp, VERSION 3.3.1 > Source code file: topio.c, line: 388 > > Fatal error: > Invalid order for directive moleculetype, file ""fad92.top"", line 15 > --- > > "Oh, There Goes Gravity" (Eminem) > > Kindly guide me to solve this problem. > Thanks in advance > > Harpreet Singh > >
Re: [gmx-users] How to generate GRO and TOP file for high-number-atom polymer?
Hi Wu Yanbin, Define the polymer building block and add it to the residue database file of your liking (ff*.rtp). Then you can use pdb2gmx to build the topology of your polymer chain. Do take some time to understand the .rtp file/entry format. Best, Tsjerk On 11/8/06, WU Yanbin <[EMAIL PROTECTED]> wrote: Hi, Genearlly I generate GRO and TOP file for polymer using PRODRG. But PRODRG does not work when the atom number of the polymer exceeds 300. So can anyone recommend other software and method? Thanks. Yours Sincerely, WU Yanbin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Tsjerk A. Wassenaar, Ph.D. post-doc NMR, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] What if the atom number exceed 99999 for Gromacs file?
Hi, Atom numbers in structure files are not used. Atoms read from a file are given fresh numbers from 1 through N, where N is the total number of atoms. Best, Tsjerk On 11/9/06, Viswanadham Sridhara <[EMAIL PROTECTED]> wrote: I believe, It does not matter. On 11/8/06, WU Yanbin <[EMAIL PROTECTED]> wrote: > > Hi, > I built up a box of polymer with box size 20x20x20 and then solvate the box with water using Genbox. Thus the total atom number exceeds 9 and I found that the atom number starts from zero when it exceeds 9. Does it matter for the ongoing command "grompp" and "mdrun"? Thanks. > Yours Sincerely, > WU Yanbin > > -- > --- > WU Yanbin > Department of Mechanical Science and EngineeringEmail: [EMAIL PROTECTED] > 3323 Beckman Institute Phone: (217)819-9064 > University of Illinois at Urbana-Champaign > 405 N. Mathews Avenue > Urbana, IL 61801 > --- > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > > -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Tsjerk A. Wassenaar, Ph.D. post-doc NMR, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] question about energy fluctuation
Mark Abraham wrote: Qiao Baofu wrote: Hi all, After running a MD of a system with about 17000 atoms, I calculated the potential and the total-energy: * Last frame read 1557952 time 1557.952 Statistics over 1557953 steps [ 0. thru 1557.9520 ps ], 2 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -273047626.559611.258 -0.305998 -476.731 Total-Energy-184656839.662828.307 -0.305999 -476.731 * I found that the Fluct./Average is 0.45% (Total-Energy), 0.22%(Potential). In the simulation, the time step is 0.001ps, and I saved the energy every step. On the other hand, on page 98 of the book "Computer Simulation of Liquids" (M. P. Allen & D. J. Tildesley), it is said "For a simple Lennard-Jones system, fluctuation of order 1 part in 10^4 are generally considered to be acceptable." This book was written nearly 20 years ago, so take with a "grain of salt" its advice on "general acceptability". Was this a simple Lennard-Jones system? If not, you are comparing apples and oranges anyway. The book is fine, but limited to LJ systems. Therefore Mark's question is important. The ratio obtained from Gromacs are quite bigger. Therefore, I want to know if there are any standard for different system to check whether the system are accetable or not. PS: Another question: I found only when the energy data are divided by the number of the molecules, the obtained result are consistent with the date in some related papers. In Gromacs, the unit of energy is KJ/mol. If divided by the number of molecules, how to consider the unit? kJ/mol per molecule? :-P The conversion is straightforward, but you may find it easier conceptually to convert your other sources into kJ/mol. You can divide by the number of molecules using g_energy -nmol. The reason GROMACS doesn't do it for you is that it is well defined only for monomolecular systems. The energy you get is hence kJ/mol system. Where system is your complete system, be it 125 argon atoms or a large biological complex. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 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] NPH simulation, constant enthalpy?
Adrien Leygue wrote: Dear Gromacs users, I have been trying to run an NPH (constant pressure and enthalpy) simulation of a LJ fluid (as a first test) with GROMACS. From what I understand (from the GROMACS manual and references therein), one can do that by considering a Parrinello-Rahman pressure coupling (and no thermostat). However, when I compute the enthalpy a posteriori using g_energy, it is far from constant and actually fluctuates a lot. But from the Nosé & Klein paper (cited in the manual, in the section on pressure coupling) it seems that I really should have a constant enthalpy, except for small fluctuations (associated to the degrees of freedom of the barostat, I believe). So I'm probably missing something. If anyone has ever tried similar simulations with Gromacs, I'd very much like any input or advice you might have on what I might be doing wrong. Thanks a lot. Adrien. You should have constant total energy, not potential (and that is only if you have no artifacts due to cutoff etc.) -- 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 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] question about energy fluctuation
Thanks. but the g_energy -nmol can only give the Bond,Angle data divided by the nmol, for the Proper-Dih. LJ, Coulomb, Potential, Total-Energy, g_energy -nmol 981 gives the same result as without -nmol 981, in which 981 is the number of molecules.I am using Gromacs 3.3.1. You can divide by the number of molecules using g_energy -nmol. The reason GROMACS doesn't do it for you is that it is well defined onlyfor monomolecular systems. The energy you get is hence kJ/mol system.Where system is your complete system, be it 125 argon atoms or a large biological complex.>> Mark> ___> gmx-users mailing listgmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> 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, Swedenphone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced Studies Max-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
