Dear Justin, Thanks for the advice, will try to follow using grace.
Ram On Wed, Oct 21, 2009 at 8:25 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: >> >> 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: >> > > I would suggest writing a script. I think plotting tools like Grace can > also extract minimum values from data sets. If the values are so close > together, then ask yourself whether the lowest of these values is > significantly different from any of the other conformation. Also, an RMSD > analysis will tell you how much the structure has changed (or is changing). > >> 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. > > Close. You also need to use -s when interconverting formats (I believe), > and -dump is not given a frame number, but rather a time in ps. > >> >> Thanks, >> >> Ram >> >> >> On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul <jalem...@vt.edu> 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 gmx-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 >>> >> > > -- > ======================================== > > 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 gmx-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 list gmx-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. 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