Hi Albert, A simple script to run:
1) a short simulation 2) g_dist/gmx distance 3) g_analyze/gmx analyze 4) decide to continue the simulation from the final coordinates or restart the simulation from the initial coordinates should do the trick I think to reproduce the SuMD method given in the first paper you originally linked to. I've not done it myself though. Cheers Tom ________________________________________ From: [email protected] [[email protected]] on behalf of Albert [[email protected]] Sent: 08 December 2015 13:51 To: [email protected] Subject: Re: [gmx-users] supervised MD in Gromacs? Dear Joao: thanks again for such kind comments. I know Plumed can perform similar work probably if we define the distance between the ligand and binding pocket as the CV. However, I am not so sure whether such kind of metadynamic simulation will lead to a nice ligand binding mode in the end, since we can place the ligand with countless pose..... In the mentioned "supervised MD", it seems that at least they can reproduce the ligand binding mode observed crystal structure in such a short time...... Do you know any other similar methods can do this? Thanks a lot Albert On 12/08/2015 02:46 PM, João M. Damas wrote: > Dear Albert, > > Unfortunately, the methods section of some papers does not reflect every > detail of what was done to achieve the results. In the particular case of > computational papers, this means the use of scripting (or even hacking) to > assist a more wide-spread code (like GROMACS). That being said, I do not > know what was done in those papers. > > I have not read the papers, but these "supervised" techniques seem fairly > similar to the milestoning ones. Maybe find an alternative there? > > Best, > João -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
