Quoting Monika Sharma <[EMAIL PROTECTED]>: > Hi!! > Thanks for suggestion. But still the problem is that whatever literature > i have, I could just get the way that they just did replica exchange at > these or that intervals. But still couldn't get clear the protocol of > doing replica exchange using Gromacs. That's why i wished for some > pieces of advice from the experts who have successfully implemented REMD > using Gromacs.
I haven't done a lot of REMD, so if someone out there has better ideas about how to do it, I hope they will add to what I'm going to tell you. It is pretty simple to set up your MD runs to do REMD. Make a set of .mdp files, each specifying a different temperature that you wish to use. Number the output .tpr files according to index, from 0 to whatever (i.e., if you have 10 different temperatures you would have md0.tpr, md1.tpr...md9.tpr). The interval for replica exchange is given by the mdrun flag -replex (refer to the manual, it's all in there). The -np flag for mdrun must agree with however many .tpr files you have (i.e., 10 for the above general example using md0.tpr through md9.tpr). As was explained in a post just a few weeks ago, nomenclature for the input is critical to getting mdrun to work. Your command line would be: $ mdrun -s md.tpr -np 10 -replex (number of steps) (followed by whatever output options) That way, mdrun will find all of your md*.tpr files. Hopefully this helps. Again, I've only done a few REMD runs, so others may have more details to add. -Justin > Thanks a lot.. > Regards, > Monika > On Fri, 2007-11-30 at 14:27 +0200, OZGE ENGIN wrote: > > Hi Monica, > > > > I had not found a detailed tutorial about it; however, you can search for > papers in which the simulations are performed via REMD.This will be helpful. > > > > Ozge. > > > > -----Original Message----- > > From: "Monika Sharma" <[EMAIL PROTECTED]> > > To: [email protected] > > Date: Fri, 30 Nov 2007 17:04:07 +0530 (IST) > > Subject: [gmx-users] Replica Exchange MD using Gromacs > > > > Dear All, > > > > I am trying REMD for the first time using Gromacs. But I am not finding > > any much helpful material regarding the replica exchange using Gromacs. > > Can anyone who has done REMD please let me know about any good tutorial > > where I can understand the way this replica exchange work in gromacs and > > the right protocol to do so.. > > > > Thanks a lot in advance.. > > > > Regards, > > Monika > > CCNSB, IIIT, > > Hyderabad. > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [email protected] > > 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 [email protected] > 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 [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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
