Thanks Justin. I tried the simulation with Protein_GDP and Water_ions, considering that "Water_and_ions" group will include MG. But it didn't work showing an error,saying "One atom not present in the coupling group". Shall I try to include MG in Water_ions group via make_ndx ?
---- Neeru neeru sharma wrote: > > Dear Gromacs users, > > > > > > I am simulating a system containing a protein with covalently attached > > Mg in complex with GDP. > > > > For nvt equilibration, I have taken protein+Mg+GDP as the single group > > and Water+ions as the other. The corresponding block from the .mdp file > > is below: > > > > -- ; Temperature coupling is on > > tcoupl = V-rescale > > tc-grps = Protein_MG_GDP Water_and_ions > > > > > > > > Is this coupling method correct, to treat Protein and Mg as different > > quantities? > > > > You are not treating them differently; they are in a merged group. Note, > though, that the default "Water_and_ions" group will include MG, and thus > grompp > with throw a fatal error. You'll have to create a custom group for this > one, as > well. Otherwise, the approach seems reasonable to me. > > -Justin > > -- > ======================================== > > 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
