Hi Justin, Thank you very much for your quick reply.... It is really encouraging to get such response For the answer of third question, How can I assign different random velocity ? Is it like assigning the different force-field ? Please elaborate or suggest some reference if you can ?
With Thanks, Vivek 2008/9/10 Justin A. Lemkul <[EMAIL PROTECTED]> > > > vivek sharma wrote: > >> Hi Everybody, >> >> I am running MD simulation for getting various conformation of a molecule, >> that can act as better receptor for docking purpose. >> While doing so, I got a number of doubts. >> Firstly what should be the range of time step I can keep in .mdp file >> (right now I am using .002 ps of time step, Can I increase it further ?) >> > > That depends largely on your force field and whether or not you're applying > constraints. For protein simulations (with constraints), 1-2 fs is pretty > standard; some UA lipid simulations use 4-5 fs. > > My second question is for how long I should run my simulation to get >> various conformation (or what is the time interval that can be taken as in >> general after which biomolecule can change their conformation ?) >> > > There is no simple answer to this question. Sampling is always an issue in > MD. Some conformational changes occur on the nanosecond timescale, others > in excess of several hundred ns, or even a few microseconds! Perhaps your > system alters its conformation rapidly, such that changes can be observed in > a few ns, but that is for you to determine :) > > How should I pick up various conformation from the mdrun that can make a >> sense ? >> >> > Probably the best idea (IMHO) is to run several simulations, each starting > from different random velocities. Run each for the same length of time and > compare the results. Do all the simulations wind up giving you the same > thing? Are there substantial differences in the conformations? > > As for extracting conformations along a trajectory (using trjconv -dump), > this may or may not be relevant. What if a certain conformation occurs once > for a single frame in one trajectory, but never again in ten other > trajectories? Do you care about that frame? Probably not, based on > reasonable sampling. What if a certain conformation occurs a few times over > a few trajectories? How do you determine its relevance? Such are the > challenges of simulation. > > You can use g_cluster to do RMSD clustering to determine which > conformations are similar along the trajectory. Whether or not any of these > "make sense" is entirely up to you and what you know about your system :) > > -Justin > > I know the questions are not strictly related to gromacs. my apologies for >> putting such questions. >> >> If anybody has insight into these questions, please reply. >> >> >> With Thanks, >> Vivek >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list 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] >> 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 list 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] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
_______________________________________________ gmx-users mailing list 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] Can't post? Read http://www.gromacs.org/mailing_lists/users.php