Dear Justin. Thanks for the suggestion, definitely i would run next time for a longer time 2-10 ns. Here, I want to learn the analysis part of the mdrun, In order to locate the lowest energy frame I executed command g_energy -f md_0_1.edr -o PE.xvg and the output was
Statistics over 500001 steps [ 0.0000 thru 1000.0001 ps ], 1 data sets All averages are exact over 500001 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Potential -1.2189e+06 1115.54 1070.01 -1.0927 -1092.7 then I had a look at the PE.xvg file, but the values are very close to identify the lowest energy point, i also tried to a have a look at the md_0_1.log file, here also it is tedious and time consuming and the values are close to remember. Can you suggest me how to locate the lowest energy frame, so that i can use the comand (below) to retrieve that particular frame coordinates in PDB file: trjconv -f md_0_1.xtc -o LEconf.pdb -dump framenumber (any frame number- corresponding to the lowest energy) and also please tell the whether the command i am going to use to retrieve the lowest energy configuration is correct. Thanks, Ram On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul <[email protected]> wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the suggestion and advice. >> As i have used a modelled protein and want to obtain the lowest energy >> configuration of the protein by doing dynamics, i want to collect the >> structure (coordinates in pdb) representing average of all the >> frames/configurations produced in MD and also the lowest energy >> configuration structure (coordinates in PDB) produced during the >> simulation, which can be used for docking. Please help how to obtain >> the average structure as well as the lowest energy configuration >> structure. >> > > Average structures are not always meaningful (or even physically-relevant): > > http://www.gromacs.org/Documentation/Terminology/Average_Structure > > You can get average structures from, i.e. g_cluster -cl, if you want. As > for the lowest energy structure, analyze potential energy, and dump out the > frame corresponding to the lowest point. Hopefully you saved coordinates > and energies at the same interval :) The potential energy will correspond > to that of the system, but hopefully it should give some indication of the > lowest energy configuration. I don't know anything about your system, but > it will also depend on how much the energy fluctuates as to how relevant > this structure might be, and how different it might be from an "average." > > If your structure comes from some model you built, realize that 1 ns is an > exceptionally short time frame, especially given the capabilities of modern > hardware and the speed of the GROMACS code. You may want to consider > running a bit longer to ensure that you really have a stable system. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
