Hello Justin, In my topology file I am declaring: --------------------------------------------------------------------------------------------------------------- ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif
; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ; Include water topology #include "spc.itp" ----------------------------------------------------------------------------------------------------------------- And in my .mdp file I am giving: ----------------------------------------------------------------------------------------------------------------- define = -DSTRONG_POSRES ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ------------------------------------------------------------------------------------------------------------------- But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Regards, Anirban On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Anirban Ghosh wrote: > >> Hi ALL, >> >> I want to do a MD simulation by restraining (freezing) the helical >> portions and allowing only the loop regions to move. I tried doing this by >> applying heavy restrain on the helical residues by generating a .itp file >> with the "genrestr" command with an index file containing the desired >> residue numbers. However during the simulation I am finding that the entire >> protein is moving. Am I doing anything wrong? Or is there any other way to >> freeze a portion of a protein? Any suggestion is welcome. thanks a lot in >> advance. >> > > If your protein is still moving, then you aren't correctly applying your > position restraints. Without seeing your topology and .mdp file, there's no > way to know what you're doing wrong. > > You can also use the freezegrps option in the .mdp file, but then you also > have to make sure you're using the appropriate energygrp_excl, etc. It is > generally much easier to apply position restraints. > > -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/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 >
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