Re: [gmx-users] diffusion coefficient
10 ps is too short of a trajectory, even for such a large system (for pure water it is considered large). i would guess that it is a typing-error and you ran for 10 ns? omer. On Wed, Feb 10, 2010 at 11:05, Amit Choubey kgp.a...@gmail.com wrote: I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I equilibriate the system for a ns and then run for additional 10 ps for analysis. Here are some of the numbers that i get -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trajectory info
See for example eq. 19 20 at JCP 129, 84505 ( http://dx.doi.org/10.1063/1.2968608). Is this what you meant? Omer. On Mon, Dec 14, 2009 at 06:56, Mark Abraham mark.abra...@anu.edu.au wrote: I think that the problem comes from pbc handling for molecules splited across boundaries - I expect : do something before calc_xcm. I could run trjconv before run tool, but I 'd like to use the original trajectories and handle them correctly. Any suggestion is appreciable. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Simulation at unrealistic temperatures
Maybe the system is exploding? Have you looked at the movie? And I agree with you that it might be unrealistic to do simulation at 600K using a force-field which was parametrized at 300K. Omer. On Thu, Nov 26, 2009 at 05:56, Neha Bharat Gajaria n.gandh...@gmail.comwrote: Dear List, I m trying to run an NPT simulation at 600K which looks unrealistic. I m running minimization followed by anealing and then NPT simulation (mdp files are attached). The job keeps running but after 162 ps, the CPU usage gradually decreases to 26% without any further output. Your help is very much appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Normalization in g_rdf
On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek ondrej.marsa...@gmail.comwrote: Dear all, I would like to understand better the way g_rdf performs normalization. I have two unexpected results: 1) In a simple simulation of atomic ions in water in a cubic box, I get RDFs that clearly reach a constant value at large enough distances, but that value is somewhat lower than one. The simulation is NpT, could that be a problem for the normalization? g(r) should fluctuate around 1 at large distances, say 9 Angstroms for pure water. 2) In a simulation in a dodecahedron, I get an unexpected decrease in the RDF at larger distances (for free ions in solution). Is there some know problem with normalization in triclinic cells? Is the RDF perhaps not truncated soon enough? Try calculating it for much larger distances, if you have PBC this should not be a problem even with the current docecahedron. --Omer. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_msd = The MSD and periodic boundary condition
On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin chihying2...@gmail.com wrote: So, how can I remove the periodic boundary condition to get the truly movement of the atoms between the two time steps ? Removing PBC and placing atoms back into their true location is easy. In general, if an atom has moved more than half of the box between two consecutive timesteps then it has jumped over the box. You can see for example eq. 19 20 in doi:10.1063/1.2968608 . --Omer. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Decreasing MSD of ligand ?
Is the decrease occurs in the long times? Omer. On Tue, Nov 17, 2009 at 21:08, Chih-Ying Lin chihying2...@gmail.com wrote: HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I simulate the protein and ligand system and then calculate the MSD of the ligand. Then, i drew the plot of the time evolution of the MSD. But the the MSD decreases as time for some period. I see nothing about my codings. Would you please tell me about any possible errors i made? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rdf and number of atoms to include
On Thu, Oct 22, 2009 at 05:17, Enemark Soeren ch...@nus.edu.sg wrote: Ahh, now I understand - sorry, Omer! No problem, glad to help. In fact, I have compared all three single hydrogen RDFs and they are identical and also relatively smooth. Since, however, with 3 times more data points (all three hydrogen atoms taken together) I get a different RDF, would that indicate that I do not have enough data after all? See my previous answers for some checks you can do on the convergence. You have to look at your data and decide if the differences are acceptable by you. I could suggest, for example, RMSD between curves, focusing just on the first peak. Are RDFs known to be slow to converge? A wild answer would be no, but thats basically depends on the size of your bin. A bin of 0.5 Angstroms would mean in each bin you'll probably have enough molecules for the data of this bin to converge, but than the curve itself wouldn't look smooth (even if it is converged). A bin size of 0.1 is often used. I have about 1000 water molecules and about 50+ glycine molecules, simulated for 10ns with 1ps sampling intervals. That should give me 500,000,000 data points for the distribution, right? Can I compare this number with the literature in which RDFs for, say, water-water interactions are reported? With 50 glycines you basically average 50 curves together, but the number of water molecules does not effect the statistics of the glycine RDF. The number of waters does mean that you most likely have a large enough system. As for water-water RDF, I think you should have more then enough data here. Just make sure when comparing to similar variables with the literature (potential, temperature, binning...). I would also worry about calculating my water-water RDF for a water which is close to glycine if I wanted to compare bulk water. One important point, which was not really clear to me before was if, provided that I have enough data, the RDFs should be identical no matter whether I use 1, 2, or 3 hydrogen atoms for generating the RDF. As far as I understood, both yours and Omer’s responses indicate that the RDFs should be identical. Did I get that correctly? From the top of my head I would say yes, you are correct. I recommend you look at some trajectory snapshots to make sure that indeed all 3 hydrogens have similar neighboring. Cheers, Omer. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rdf and number of atoms to include
On Wed, Oct 21, 2009 at 07:28, Enemark Soeren ch...@nus.edu.sg wrote: Dear users, I would like to compare interactions between molecules by using RDF. I have tried looking at glycine and water, and compare the following two interactions: 1) between the amine hydrogen atoms in glycine and the oxygen atom in water 2) between the carboxyl oxygen atoms in glycine and the oxygen atom in water However, my result in 1) depends on how many of the 3 hydrogen atoms I include in the calculations. Why is that? If you mean that when focusing your RDF calculations on either one of the three hydrogens results in three different RDFs then it means that each hydrogen feels water differently. I bet this difference is only for the first peak of g(r) and the other peaks overlap between the three RDFs. As for how reasonable this result, its not unlikely because glycine has atleast 2 different types of hydrogens (say, C-H vs. N-H), depending on the protonation state. You might want to provide more details on the system you are studying to get better answer. I am assuming that the RDFs are converged so that including more trajectory data and/or sampled molecules and/or changing bin size does not result in a drastic change to the curves. Does that mean that I cannot directly compare the strengths (RDF peak height) of the two interactions as they are not based on the same number of atoms? Does it also mean that I must always calculate RDFs by using 1 atom on each of the particles/groups that I am comparing? I am not sure how good it is to use the first peak of g(r) to analyze strengths, but you should also consider the width and area under peak. This peak is an average on all nearest neighbours, bonded or not, so it might not give you a good estimate of the hydrogen bond, for example. If you are unsure of your g(r) calc it just for water (that is - only oxygen-oxygen of water-water). At long distances (~10 Angstroms) it should fluctuate around 1. Bests, Omer Markovitch. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] reduced units
On Sat, Oct 17, 2009 at 06:10, lammps lammps lammp2fo...@gmail.com wrote: Dear, I want to do stochastic simulations in the framework of Langevin dynamics using Gromacs with the reduced units. The questions are: 1. How to turn on the reduced units? Is there any parameters for setting? I am not sure I understand. For Langevin dynamcis/thermostat use: integrator = SD bd-fric=0; Read the manual about the relations between dt tau-t, I use 5e-4 2, respectively. Hope I helped. Omer. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Making Commands Non-Interactive
Have you tried: echo 0 zero trjconv bla bla bla zero You could put more arguments in the file, for example - use the -center option, and then echo another 0 into the zero file. --Omer. On Sun, Oct 4, 2009 at 18:22, ABEL Stephane 175950 stephane.a...@cea.frwrote: Dear GMX Users, echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in loading xtc in VMD
For VMD you first load a GRO (or pdb) file, and then XTC. The XTC file should contain _exactly_ the same number of atoms as the GRO file. Did you save the entire system in the XTC, or just a specific part of it? Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 2, 2009 at 20:39, Paymon Pirzadeh ppirz...@ucalgary.ca wrote: Hello, I ran an NVT simulation from a minimized configuration. The simulation ended normally and I have a final configuration as well. But, when I load the initial coordinates and then I want to add data, which is the xtc file, nothing happens! no frames are loaded. This is while the xtc file has a reasonable size and when I load it individually in VMD, it loads the exact number of frames it should (300 frames). Is something wrong with my outputs or is there something with VMD. This is the second system I have such a problem. Regards, Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] option for finding forces between two groups
Work with groups and an index file, and define energy_groups in the mdp file also. For indices, check make_ndx utility. Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 2, 2009 at 20:31, Pradip Biswas biswas...@gmail.com wrote: Hi, Anyone can please tell me whether there is any option in GROMACS to find forces between two groups (say for example, between two residues in a protein or between a peptide and a residue in a Protein for Protein-peptide interaction) or one need to workaround with the code to get that? Thanks in advance. Biswas. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parameter to for randomizing simulation
If you are performing LD then setting ldseef=-1 does the trick. For MD, try genseed as suggested. I believe the manual explains all, including the range issue. Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Tue, Sep 29, 2009 at 19:31, Jack Shultz j...@drugdiscoveryathome.comwrote: I thought there was a way to introduce the random number generator via the application I was trying to use this parameter Id_seed=-1 but it failed :-( I suppose I can insert a random number to gen_seed every time I submit. is there a range of numbers for gen_seed? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about energy minimization
Trj trjconv -pbc nojump, or trjconv -h and read the short help printed. Omer. I actually didnt realize this until i did a long simulation after which the trajectories of some of the atoms looked way out of the box dimensions. The co-ordinates of many atoms didnt lie in the box range. Although the output file contained the same box dimensions as I started with. Could someone help me in understanding what happened? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Trajectory files in vmd
How do you run vmd? The first argument should be a GRO or PDB file, and the second argument is the TRR or XTC trajectory. Alternatively, you can open a new molecule in vmd and than load data into that molecule. --Omer. On Thu, Sep 24, 2009 at 08:21, Aditi Borkar aditi.bor...@gmail.com wrote: Dear All, When I am loading the GROMACS trajectory in VMD, I cannot the evolution of the protein structure with time. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] 1-4 interaction between atoms in PBC mode
I assume that atoms from opposite ends of the simulation box are being seen by GROMACS as being 1-4 neighbors as a result of the PBC, Are you sure? have you looked at the last good frame before this message? GMX treats PBC as it should during MD neighbour search, so maybe this is a pair that was initially close and interacting, but later moved away from each other. but the shortest distance between the atoms is not being observed. Is this the problem? Is this problem resulting in the system exploding? And, how do I resolve this problem? If you are sure that everything else is ok, then extend the table extension. Two other things to work around this are either reduce timestep or check that your definition of the box is as it should. --Omer. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Large fluctuation of protein temperature with nose hoover thermostat
The group PROTEIN isn't very large as the group NONPROTEIN, therefore its total kinetic energy fluctuates more. --Omer. On Wed, Sep 16, 2009 at 12:10, Stephane Abel stephane.a...@cea.fr wrote: tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.4 0.4 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 310 2.46886 2.46886 6.12135e-07 0.0171398 T-Protein 310 32.1134 32.1117 -4.10352e-05 -1.14898 T-Non-Protein 310 2.47549 2.47548 8.55869e-07 0.0239643 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] table extension
Thanks Mark. I am simulating a dimer in vacuum, and it is my understanding that once a non-bonded interaction has exceeded the table-extension cutoff this interaction will NOT be included in the potential for the remaining simulation, even if it will later come back to a distance within the table-extension. Your answer helped me. It is now a matter of choosing the box dimensions table extension that will be reasonable yet not increase the computation time too much. --Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Wed, Aug 26, 2009 at 16:03, Mark Abraham mark.abra...@anu.edu.au wrote: Probably not... if you're asking this question because you suspect something's not working properly, you might get enlightenment/a fix quicker if you're more explicit :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] table extension
Thanks. And what happens if later on it comes back to the cut-off + table-extension range? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 11:13, Berk Hess g...@hotmail.com wrote: A interaction beyond the cut-off + table-extension will get a random energy and force depending on what is stored in the memory of your computer beyond the table ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] table extension
But what if the gmx code did notice it? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 16:21, Mark Abraham mark.abra...@anu.edu.au wrote: It would look up a non-random energy and force. If the code never noticed the distance was out-of-range, it won't notice it come back into range either. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] table extension
Dear GMXs, I would like to clear something out, for myself: The table extension given in MDP file applies to nonbond_params pairs interactions which are specified in the TOP file (and also electrostatics)? Is there an interaction which does not use the table extension (other then bonds, angles dihdrals)? I have read the manual. Thanks, Omer. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Periodic Boundary Condition Issues
Try combining indices with that, use make_ndx -h. --Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Wed, Jul 22, 2009 at 18:27, Justin A. Lemkul jalem...@vt.edu wrote: The trjconv -pbc options were designed to fix this sort of issue. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Protein going out of the box
Try using trjconv. Look at the -pbc options and also maybe -center options. --Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Wed, Jul 15, 2009 at 10:09, nikhil damle pdnik...@yahoo.co.in wrote: but peptide remains inside the box while protein is seen outside. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] non squares box
Dear All, I would like to ask your help on the following - I want my simulation to include a surface, and have PBC. The surface I chose is aligned on the XY plane. However, the surface is not a square. The surface dimensions are a=b=169.2 c=6.9 Angstroms, the angles are: bc=ac=90 ab=120 degrees. I have used editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0. To test this, I have used trjconv -pbc nojump -center yes -boxcenter zero. My problem is that the trjconv generates a structure where some of the surface atoms are cut and/or overlapping... Could you please help me? Wheres the problem? The input PDB I use is about 2 MB in size, so it can't be attached here. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] non squares box
I prefer to keep discussions professional, Mark and Tsjerk. Anyway, I am doing MD with PBC. I have a surface which sits on the XY axes, the surface is not a square and my question is how do I tell gromacs that I have a non standard box. Please see my original post for more details: ++ I would like to ask your help on the following - I want my simulation to include a surface, and have PBC. The surface I chose is aligned on the XY plane. However, the surface is not a square. The surface dimensions are a=b=169.2 c=6.9 Angstroms, the angles are: bc=ac=90 ab=120 degrees. I have used editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0. To test this, I have used trjconv -pbc nojump -center yes -boxcenter zero. My problem is that the trjconv generates a structure where some of the surface atoms are cut and/or overlapping... ++ Thank you. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PBC
Remember that for PBC=xyz, the neighbor search is faster, so I suggest using PBC with a very large box. --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Alternative TRP residue
How many letters for residue name are allowed in the PDB format? Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Combining LJ and buckingham potential
Hello Osmair, Perhaps you can try using the [ nonbond_params ] [ pairs ] sections of the TOP file? How did you define these interactions in your TOP file? --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Apr 17, 2009 at 22:51, osmair oliveira osmai...@hotmail.com wrote: Hi, I have tried to simulate a crystal in water solvent, however I found the error: ERROR 0 [file new-topol3.top, line 19]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) So, my question: How can I use or define LJ potential (for water) and buckingham potential (for a crystal) in the same *.top, *.itp? Thanks, Osmair V. Oliveira Ph.D. Student Brazil ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
Hello. What do you mean by jump? Perhaps the connected MN is a stable state? If you'll supply more details we could try to help you better. --Omer. On Sat, Mar 14, 2009 at 08:15, Homa Azizian haziz...@razi.tums.ac.irwrote: My ion jump out of the protein after MD.My ion (MN) has not any covalant bond by its neibour, just has electrostatic intraction. is there any line that I have to add to the itp file or top file in order to prevent this problem. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] initial velocities Langevin dynamics
Thus I am a bit confused about it! I'm confused about the manual comment about only being meaningful with the MD integrator, but we'll have to wait until someone who knows something about LD can post! For LD, the velocities will (should) get rescaled by the random thermal noise, that is- by the Langivin thermostat. With MD, the thermostat works like friction (positive or negative friction). So you see, that for LD, an initial velocity of zero should next be changed by the thermostat, while for MD the rescaling shouldn't work for zero. --Omer Markovitch. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] is there a possibility to convert .gro files directly to PDB?
Use: trjconv -f conf.gro -s conf.gro -o conf.pdb. Note the use of -s on the same gro file. --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Diffusion coefficients ( Exp X Simul )
See also the work of Hummer (JPC-B (2004), http://dx.doi.org/10.1021/jp0477147), dealing with box size effect on D. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Tue, Mar 3, 2009 at 23:37, Eudes Fileti fil...@ufabc.edu.br wrote: Hello, someone could suggest me references which discusses the difficulty of obtaining values for diffusion coefficients in agreement to the experimental values? ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Turning off electrostatic or Van der Waals interactions
Why not create dummy topologies, without charges/vdw ? Another option, which I am not sure of its effect, is, perhaps, to take extremely small cutoffs. --Omer. Lee Soin wrote: I'm trying to rule out the effect of electrostatic or Van der Waals interactions while performing a simulation. Do you mean that I should modify the code and re-compile? ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Barostat Density decreasing to zero
Dear All, I have simulated a protein inside a box with water and ions. I began by minimizing my system (which has a total charge of zero), until the maximum gradient was small enough and the potential energy become negative. Then I heated it, slowly, to 300K at constant volume (using berendsen thermostat and tcoupl = 1 ps). Then I performed 500 ps NVT simulation to equilibrate the temperature, at 300K. Then, I tried to equilibrate the pressure and run NPT simulation, using Berendsen barostat (p=1, pcoupl=10) and Berendsen thermostat (T=300K, tcoupl = 0.1). My problem is, that with the barostat thermostat both active in the same MD run, my density drops to a very low value (at the first MD steps, the density is 1000, dropping later to 100 kg/m^3). That is- my box dimensions increase significantly (from around 6x6x6 to 12x12x12 nm^3. If I change the pressure coupling constant, the speed of the expansion changes but all simulation converged to a small density between 50-100 kg/m3. Your help is appreciated; Probably, I am not controlling the simulation like I should. I will appreciate any advice. Thank you, Omer Markovitch. I have used gromacs version 3.3.3, Here is my .MDP file for the NPT run: integrator = md dt = 0.001 nsteps = 50 comm_grps= system nstxout = 500 nstvout = 500 nstcheckpoint= 1000 nstlog = 500 nstenergy= 500 nstlist = 10 ns_type = simple pbc = xyz rlist= 1.0 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 epsilon_r= 80 epsilon_rf = 80 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 table-extension = 1 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes tcoupl = berendsen tc-grps = system tau_t= 0.1 ref_t= 300 Pcoupl = berendsen Pcoupltype = Isotropic tau-p= 10 compressibility = 4.5E-5 ref-p= 1 andersen_seed= 815131 constraints = none ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: How to output a single index group
Also check out make_ndx -help. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Mon, Jan 19, 2009 at 18:28, Vitaly Chaban vvcha...@gmail.com wrote: I am running a simulation of 5 time steps and am trying to avoid setting nstxtcout = 1 or nstxout = 1. The file size becomes unmanageable if I set either of these two parameters to 1. I do not need the coordinates for all atoms in the system, just the alpha carbons, which are grouped in the index file, but I do need coordinates for each time step. Is there any way of specifying in the parameter file to only output the coordinates for the alpha carbons? Thanks! ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] time of dynamic
would you please tell me for compare dynamic peptide what time for MD is enough by gromacs?generally. You can take your 20 ns simulation, and divide it into 2-4 parts, each 10 (or 5) ns long. Then, calculate the property you are interested in for each part seperately. If 20 ns is more then enought, then the difference between the parts should be minimal. Another option is to calculate the variance of the propery you are calculating, vs. time. --Omer. ___ 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] Replacing molecules in .gro coordinate file
Supposed I have a .gro file of 38 molecules of A which are already in equilibrated conformations. Now I want to transform 15 molecules of A into B therefore I will have the binary mixture of A/B with 13:15 molar ratio in the final structure. How can I do this? Any suggestions will be appreciated. Maybe open A B in vmd together, and then save them as one PDB? Omer. ___ 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] Analyzing a trajectory split over multiple files
On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty [EMAIL PROTECTED]wrote: Dear all, I have a very long trajectory split over a large number of files. What would be the most efficient way to use the analysis programs over them? Do they support multiple input for trajectory? Or I need to combine all files into a single one anyway? You should analyze each individual part on its own, and output the raw data of the result, then average the parts together. For example - say you are interested in coordination number of molecule X: For each part, output both the total number of X's found, plus the total number of X neighbors found. The coordination number is then the sum of neig. divided by the sum of X's, from ALL parts. It might be an issue if each part has different time length, then averaging the coordination number of each part might give more statistical weigh to short parts then they should have. In other words, you should first collect the data of each part together, and only then avg.. --Omer. ___ 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] small protein big frozen group - exploding
Dear, I am simulating a small protein (less then 50 amino acids) at room temperature, with no additional atoms and/or molecules and/or ions. The simulations seems to proceed ok (in terms of avg. kinetic energy and other energy terms). Then, I take the same protein, and introduce a surface to the system. My surface is just a set of identical hard sphere atoms, here is how a surface atom is defined inside my .TOP file: [ atomtypes ] ;name mass charge ptype c6 c12 X 1.0000.000 X0.000 0.600E-09 And there are 10 times more surface atoms then protein atoms. In my .MDP file, there are two energy groups: protein non-protein. The surface is frozen in all xyz directions. Now, the problem is that with the surface, my protein quickly explodes, and I have no idea why. The surface and protein each coupled to its own thermostat. Your help and ideas/comments are appreciated. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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] temperature coupling strength
On Mon, Nov 10, 2008 at 17:42, Seunghyun Chung [EMAIL PROTECTED] wrote: Deal all, Is there any practical approach to choose the right temperature coupling strength for a simulation? For example, if a system behaves differently with weak coupling and strong coupling, which result I should trust? In general, the coupling lifetime should not interfere with any fast degrees of motion you might have. For example, for pure water (where hydrogen bond lifetime is in the ps region, and OH vibration is in the fs lifetime), the thermostat coupling might be ~0.5 ps, but for a protein, perhaps a value in the area of 1 ps and above might be more suites. Plotting the temperature devations and/or averages might direct you to the better value. Also, I thought giving a very weak nose-hoover thermostat coupling would be similar to the NVE simulation. However, when I run the simulation, the system behaves very weirdly by constantly accelerating and slowing down. will there be any explanation on this behavior? I agree. But did you start applying the weak coupling before or after the system was already equilibrated? --Omer. ___ 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] stochastic dynamics , langevin
Dear All, I am trying to perform Langevin dynamics of large peptides / proteins. After reading the manual going over some old mails in this list, I have two points I hope you could clear for me: [Gromacs version 3.3.3] 1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the proper keywords I should use for Langevin dynamics: integrator = sd ; bd-fric= 0 ; tau_t = 10 ; ref_t = 300 ; With bd-fric=0, the friction is taken as the inverse tau_t. 2) From your experience, what are good values of tau_t (or 1/tau_t) for simulating a protein? In 2006 list, David has commented that choosing tau_t is very important ( http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ). Your help is appreciated. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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] stochastic dynamics , langevin
Thanks for the quick reply Berk. 1) Is this the proper keywords I should use for Langevin dynamics: integrator = sd ; bd-fric= 0 ; tau_t = 10 ; ref_t = 300 ; Basically, I want to know if I am using the 4 parameters correctly. That is - for Langevin dynamics, I should pick bd-fric=0, to allow the friction to be taken from 1/tau_t ? Secondly, I am looking for examples of tau_t different people use for different system. Thanks, Omer. ___ 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] range of gen_seed
I believe that (-1) as the seed takes the time or something as the actual seed, thus ensuring no two identical seeds, and no two identical velocities. Omer. On Fri, Oct 17, 2008 at 12:11, sarbani chattopadhyay [EMAIL PROTECTED] wrote: I want to know that does this ensure that the mdrun starts with diffrent velocities ? Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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] Simulation of a protein confined in a box
In short - you can apply PBC in all directions (XYZ) by choosing the proper keyword in the .mdp file, I believe the box dimensions are defined in .gro file. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 10, 2008 at 16:00, Lee Soin [EMAIL PROTECTED] wrote: Maybe I didn't put it clearly. My intention is to simulate a protein confined in a box, and the problem is that I don't know how to define a boundary, or a wall, in GROMACS. ___ 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] Simulation of a protein confined in a box
Oh, I didn't read carefully. My suggestion would be, perhaps, to physically put atoms on the sides of the box (possibly, fill each side completely), and to place on them very high repulsion. You might want to freeze them up, and exclude their self interactions from the energy calculation. Good guess Suman. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty [EMAIL PROTECTED]wrote: Possibly what he is interested in is a system WITHOUT PBC? I don't think with PBC the system is really confined, since there is no true wall to reflect the colliding molecules. Thus to study the effect of real confinement, it is necessary to remove PBC and impose reflective boundary conditions. I am only guessing! :) --Suman. ___ 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] Simulation of a protein confined in a box
Boundary should not precisely be around the protein, otherwise some parts of the protein would feel other parts via the boundary. In general, if you apply periodic boundary conditions (PBC), take the dimensions as such so the protein would NOT feel the PBC. Say you have an unfolded protein (or a MD during which a protein unfolds) whose length is about 20 Angstroms, and you use no explicit solvent. You might not want to take the dimension of the box to be smaller they, say, 40 Angstroms. Its just an example. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 10, 2008 at 11:03, Lee Soin [EMAIL PROTECTED] wrote: But the problem is: how to define a boundary? ___ 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] trjconv - converting trajectory into a pdb
Hello, I have ran some MD with GROMACS v3.3.3, and used the command trjconv -f traj.xtc -o traj.pdb -s file.gro to generate a pdb movie. My simulation includes charged atoms in some residues, but the output pdb does not seem to include the formal charge data. My question is, is this a known issue (that GROMACS does not print the charge info. in the pdb), or, perhaps, it is a symptom of something I did wrongly? (its not a big deal, but still - it would be nice to have this data directly in the movie) Thank you for the help, Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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] HB lifetime
Please see my comments below. Hi, The HB definitions and associated lifetimes are a bit arbitrary, so there' s always going to be some ambiguity here. That being said, the reason the integral of the HB correlation function C(t) isn't an ideal definition is that C(t) is only roughly exponential. Same argument goes for getting the lifetime from a fit to C(t), or looking for the time where C(t)=1/e, or similar simple approximations. I disagree. HB lifetime is only slightly dependent on the exact values of the geometric parameters, around the usual values of R(O...O)= 3.5 Angstrom angle(O...O-H)= 30 degrees, please see JCP 129, 84505 (a link to the abstract is given below). C(t) of a HB obeys the analytical solution of the reversible geminate recombination (see a short review in JCP 129), and so its tail follows a power law: C(t) ~ Keq*(D*t)^-3/2, which is indicative of a 3 dimensions diffusion. What Luzar recommends is to think about an equilibrium between bound and unbound molecules, so that they interact with a forward and a backward rate constant k and k'. k gives the forward rate, ie. the HB breaking rate, and k' gives the HB reformation rate... they are not equal due to the diffusion of unbound molecules away from the solvation shell. There are a few advantages of going this route, not the least of which is that you tend to get similar lifetimes regardless of small changes in the HB definition, and whether you use geometric or energetic criteria, etc. The reversible geminate recombination deals with the A+B --- C, here A=B=H2O C=(H2O)2, the bound water dimer. From a single fit to C(t) one receives the bimolecular forward backward rate constants, which are well defined. k' you suggest is an apparent unimolecular rate constant, which appears to be more suited for short times. Extracting these rate constants is a bit tricky (I usually do it by hand), but I guess gromacs has a scheme to do it... I haven't actually looked at it (though I really should!). I'd recommend some caution though, a scheme that works well for HB's between water molecules in bulk may need to be adjusted to properly model HB's between water and polar atoms. I have to disagree again. The A+B=C problem has an analytical solution. Technically, ones only need to know how to calculate an error-function and to solve a cubic equation, please see eq. 9, 10 at JCP 129. The geminate problem is robust in the sense that it describes C(t) of ANY 2 particles, as long as their behavior is controlled by diffusion, it describes the water pair, but should describe also, for example, liquid argon. For the second case, ofcourse, different rate constants are expected. One should NOT see JCP 129 as a proof that previous works were absolutly wrong ! Instead, it shows that the postulate by Luzar Chandler, that C(t) of water is controlled by diffusion, is right, and that with the analytical solution of the geminate problem one can understand some aspects of the water dimer. For example - what causes the activation energies of the forward backward rate constants to be about similar rather then being different by the strength of 1 HB? Hope I was clear. Omer Markovitch. ** a link to JCP 129, 84505 (2008) http://dx.doi.org/10.1063/1.2968608 ** supporting information includes a short trajectory movie ___ 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] Hydrogen Bond Lifetime
Please see also my reply under HB lifetime to Christopher Daub. I think that JCP 129, 84505 (2008) should be read when dealing with C(t) in general HB lifetimes in particular. ** link: http://dx.doi.org/10.1063/1.2968608 Omer Markovitch. ___ 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] Fwd: charges,resonance and electrostatics
Hello, There is a point, I want to clear out for myself: Say we focus on the aspartate residue. It has a formal charge of -1. This charge on either oxygen of the carboxyl is -0.8 (oxygens OD1 OD2), according to one of the force fields employed in GROMACS. What is the right way to calculate electrostatics here: 1) As is, and letting the two oxygens repel one another. 2) Ignore this specific pair when calculating? How does GROMACS operates? I think that (1) is the common practice, but I want to be sure. Thank you, Omer Markovitch. (this email was sent to gmx-dev. by mistake) Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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] Fwd: charges,resonance and electrostatics
There is no non-bonded interaction between these two oxygens, unless you are using an Urey-Bradley potential for the angle, like in the CHARMM force field. Most (if not all) of the standard force fields in Gromacs treat the interaction of these oxygens within an angle definition, which is a bonded term. -Justin So no coloumb law between the two oxygens? 10x, Omer. ___ 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] searching the archives
Shalom, Is it just me or there is a bug in the archives search page http://www.gromacs.org/search ? (error 404 - page not found) --omer. ___ 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: Time step in md
On Sat, Sep 20, 2008 at 10:29, Vitaly Chaban [EMAIL PROTECTED]wrote: could you explain my the secret of choosing to time step for md integrator? The secret is, to have the timestep small enough so that you could truly say between two consecutive steps the forces are linear, and to have it large enough so the computation would be feasible. Other then that, look at the previous answers you got for a more hands on approach. You might also want to read about integrating MD. --Omer Markovitch. ___ 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] GROMACS sample procedure
I think there are example files, look at the gromacs web site. A super brief answer would be as follows: File.top is the topology file. It holds description of atom types potentials. File.gro holds the initial coordinates, and box dimensions. File.mdp holds run parameters (how many steps, temperature, output control, simulation type, etc`). The command grompp reads some input files, and prepares file.tpr, which is then used as an input to mdrun - the ultimate command that does the actual MD. The number of different initials of G.R.O.M.A.C.S., minus the nearest prime number is 17. Gromacs has healing powers. Please refer to the gromacs manual for more details, and to the gromacs wiki aswell. Omer Markovitch. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Sep 18, 2008 at 12:03, Christopher Ambe [EMAIL PROTECTED]wrote: I am new to GROMACS and have not tried any calculation using it. I have installed grmx on scientific linux. Can anyone help me find a sample procedure of using GROMACS for molecular dynamics simulation (or even for simple energy calculation)? I am interested in doing research on Molecular Dynamics using GROMACS, but so far, I really dont have an idea where to start. I hope to hear your advise. Thank you very much Christopher Ambe MSU-Iligan Institute of Technology ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] kill some atoms
What is the reason for shrinking the box? If it is for technical reasons, for example - nicer visualization etc`, then perhaps this could be done manually. If you plan to use the smaller box later, then maybe you could do some part of high pressure simulation, to reduce box size while keeping it physical. --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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] defining group
Hello, I would like to ask for your help in defining groups: Say I have a protein. I would like to have two groups (1) the Calpha backbone (2) everything else. Later on, I will want to freeze the Calpha group. How can I define these groups? Where? I have looked in the manual, but I do not understand how to do it and in which files. Thank you, Omer Markovitch. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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] defining group
Thank you both! Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Sat, Sep 13, 2008 at 15:57, Justin A. Lemkul [EMAIL PROTECTED] wrote: Omer Markovitch wrote: Hello, I would like to ask for your help in defining groups: Say I have a protein. I would like to have two groups (1) the Calpha backbone (2) everything else. Later on, I will want to freeze the Calpha group. How can I define these groups? Where? I have looked in the manual, but I do not understand how to do it and in which files. Groups are defined in index files (.ndx), which are created with make_ndx. Calpha is a default group read in from a protein structure. To create a group that is everything but Calpha (group 3 in the make_ndx list), you would use !3 at the make_ndx prompt. -Justin Thank you, Omer Markovitch. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: optimizing the mailing list
Using emails, this might be done manually - each user will add to the TOPIC something like: tag install, etc`. Then each user could define his own rule, in his personal email account, how to deal with messages that contain tag xxx gromacs in the topic. Just a thought... Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Mon, Sep 8, 2008 at 21:17, David van der Spoel [EMAIL PROTECTED]wrote: Vitaly Chaban wrote: it's called internet forum... :) we've had this discussion before. On a forum many of the hardcore gromacs people (like me) would probably not respond anymore. I suggest that we consider ways in which the mailing list can be optimized. My initial thought is to allow submitters to flag messages as belonging to some particular topic(s). e.g. program crash force fields protein free energy coarse graining lipids and detergents unknown etc. Since the submission is by regular email and hence there is no possibility of introducing a radio box with topic options, this could be implemented by allowing any user to define the topic to which a particular message belongs. Ideally, the submitter would go to the website after submission and set the topic of their own submission. If the archives then allowed a user to view only a particular topic, then this would offer an alternative to the search tool, and also a link to such a topical list could be posted in the relevant pages on the wiki. I realize that the actual coding of such an interface may not be available at this time. But I suspect that somebody on this list knows some type of useful optimizations that are possible at this time. Chris. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to convert gromacs traj file(.xtc) to amber traj file?
Are you sure this will be done automaticaly if you'll procide gromacs with an output file called filename.trj? There is also the option of converting into PDB: trjconv -f traj.xtc -o trajtraj.pdb -s coordinates.gro. omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Mon, Sep 8, 2008 at 20:14, ranqi zhu [EMAIL PROTECTED] wrote: Hi, Everyone, I just want to use the clustering tool in amber which only take trj file. Thanks -Ranqi -- Want to do more with Windows Live? Learn 10 hidden secrets from Jamie. Learn Nowhttp://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!550F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: manipulation of trajectory data
to me too. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Mon, Sep 8, 2008 at 16:30, Vitaly Chaban [EMAIL PROTECTED]wrote: gurgo If anyone has a simpler example along the lines of my interests, gurgo please send me it! and to me... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] installation and fftw
Regarding buildit FFT - I believe they say it is slower then other packages. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Sep 4, 2008 at 21:54, Myunggi Yi [EMAIL PROTECTED] wrote: I have done the compilation. Thank you so much. On Thu, Sep 4, 2008 at 12:08 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Myunggi Yi wrote: Thank you for your answer, but I can't really get you. I am using gromacs 3.3.3. http://3.3.3 http://3.3.0.3/. on CentOS with AMD64 clusters with infiniband connection. I have both INTEL and GNU copilers (gcc4.1.2 and gcc3.4) and openmpi (intel and gnu). You are saying I don't have install fftw by myself, aren't you? Then how can I compile? What is the best option for the performance? I did the followings. == ./configure --prefix=$HOME/gromacs/ --with-fft=fftw2 make make install make clean ./configure --enable-mpi --disable-nice $HOME/gromacs/ --with-fft=fftw2 --program-suffix=_mpi make mdrun make install-mdrun == Is this wrong? Seems reasonable, did it work? Can I compile it with intel compiler? It is easy to use gcc, and definitely do *not* use gcc-4.1.2; use 3.4. There are step-by-step instructions on how to install both FFTW and Gromacs on the Gromacs website: http://www.gromacs.org/content/view/23/33/ Following these directly will give you the standard installation, in serial and parallel, and single and double precision, if you choose. -Justin I'm sorry. I have so many questions. Please let me know how to compile it. Thank you. On Thu, Sep 4, 2008 at 11:40 AM, Roland Schulz [EMAIL PROTECTED] mailto: [EMAIL PROTECTED] wrote: Hi, Gromacs has it's own parallel FFT which only uses FFTW for the local FFT. Thus a non-MPI FFTW is fine. and FFTW 3 is faster than 2. Roland On Thu, Sep 4, 2008 at 8:53 AM, Myunggi Yi [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Dear gmx users, fftw3 seems doesn't support MPI. Why is the gromacs configuration default fftw3 not fftw2? Which version should I use for parallel computing? Thank you. --Best wishes, Myunggi Yi == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi http://www.scs.fsu.edu/%7Emyunggi http://www.scs.fsu.edu/~myunggi [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --ORNL/UT Center for Molecular Biophysics cmb.ornl.gov http://cmb.ornl.gov ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Best wishes, Myunggi Yi == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] printing coords ; energies
Thank you. Sorry for not being clearer. I meant where in the source code are the energy related functions variables? Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Sep 4, 2008 at 16:19, Jochen Hub [EMAIL PROTECTED] wrote: Omer Markovitch wrote: Dear All, I would like to consult you on the following two things: 1) I have a small, preanalysis, routine I would like to run each time a frame is written and added to the trajectory file. After some checking, I believe that, in the file *stat.c*, the routine *void write_xtc_traj(FILE *log,t_commrec *cr, char *xtc_traj,t_nsborder *nsb,t_mdatoms *md, int step,real t,rvec *xx,matrix box,real prec)* is the routine actually printing each frame. Is this true or perhaps I've missed something? 2) Regarding energies - where are the energies stored? I mean the energy per type? The energies of the energy groups (as defined in the mdp file) are stored in the edr file (ener.edr by default). jochen In which file variable is this defined? I understand that these values are printed to the log file (usually named md.log), but I failed to locate the exact functions dealing with this. Thanks, Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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 -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ 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] printing coords ; energies
Dear All, I would like to consult you on the following two things: 1) I have a small, preanalysis, routine I would like to run each time a frame is written and added to the trajectory file. After some checking, I believe that, in the file *stat.c*, the routine *void write_xtc_traj(FILE *log,t_commrec *cr, char *xtc_traj,t_nsborder *nsb,t_mdatoms *md, int step,real t,rvec *xx,matrix box,real prec)* is the routine actually printing each frame. Is this true or perhaps I've missed something? 2) Regarding energies - where are the energies stored? I mean the energy per type? In which file variable is this defined? I understand that these values are printed to the log file (usually named md.log), but I failed to locate the exact functions dealing with this. Thanks, Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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
