Hello Justin, Thanks a lot for the reply. Yes, I am using GROAMCS 4.5 and my system consists of two chains of two proteins, a substrate and an inhibitor solvated in water. So can you please tell me what should be the values for: couple-moltypecouple-lambda0couple-intramolThanks a lot again.
Regards, Anirban On Sat, Nov 27, 2010 at 9:15 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Anirban Ghosh wrote: > >> >> Hi ALL, >> >> I am trying to run free energy calculation and for that in the md.mdp file >> I am keeping the following option: >> >> ; Free energy control stuff >> free_energy = yes >> init_lambda = 0.0 >> delta_lambda = 0 >> sc_alpha =0.5 >> sc-power =1.0 >> sc-sigma = 0.3 >> >> >> But still I find that in my log file the values for dVpot/dlambda is >> always coming to be zero. >> What I am doing wrong? >> Any suggestion is welcome. Thanks a lot in advance. >> >> > You haven't indicated your Gromacs version, but assuming you're using > something in the 4.x series, you're not specifying the necessary parameters > to do any sort of transformation, particularly couple_lambda0 and > couple_lambda1. If left at their default values (vdw-q), nothing gets > decoupled. > > -Justin > > >> Regards, >> >> Anirban >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/Support/Mailing_Lists/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/Support/Mailing_Lists >
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