Thanks Justin. I have tried both ways now and considering Protein_MG_GDP and Water_ions groups, it is running without any error but Protein_GDP and MG_Water_ions is failing with an error message.
Thanks again... ____ Neeru > > neeru sharma wrote: > > > > > > 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 ? > > > > I think the better approach is the one you posted before. > > -Justin > > > > > ---- > > 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 <http://vt.edu> | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > >
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