[gmx-users] Re: question about freeze

[Dr. Vitaly V. G. Chaban]

>
> I want to do a minimization and a md run with my protein. But I only want
> the hydrogen atoms to be minimized but not the rest of the protein.
> I use the
> freezegrps = Protein-H
> freezedim = Y Y Y
>
> option in my mdp files to make sure that they don't change.
>
> During the minimization steps everything works fine and it really does not
> change.
> But now I started the md run and here the protein somehow get minimized
> too. I do not understand why everything works fine during the minimization
> but not during the md run.
>
> My mdp file for the md run looks like this:
>
>
> define          = -DPOSRES
> integrator              = md
> dt                      = 0.001
> nsteps          = 5000
> nstxout         = 100
> nstvout         = 0
> nstfout         = 0
> nstlog          = 1000
> nstxtcout               = 500
> nstenergy               = 5
> energygrps              = Protein Non-Protein
> nstcalcenergy   = 5
> nstlist         = 10
> ns-type         = Grid
> pbc                     = xyz
> rlist           = 0.9
> coulombtype             = PME
> rcoulomb                = 0.9
> rvdw            = 0.9
> fourierspacing          = 0.12
> pme_order               = 4
> ewald_rtol              = 1e-5
> gen_vel         = yes
> gen_temp                = 200.0
> gen_seed                = 9999
> constraints             = all-bonds
> tcoupl          = V-rescale
> tc-grps         = Protein  Non-Protein
> tau_t           = 0.1      0.1
> ref_t           = 298      298
> pcoupl          = no
> freezegrps = Protein-H
> freezedim = Y Y Y


Eva -

Sorry, I did not get your question.

> But now I started the md run and here the protein somehow get minimized
> too. I do not understand why everything works fine during the minimization
> but not during the md run.


Your MDP file should freeze all the atoms in the "Protein-H" index
group. Are these atoms actually non-frozen during MD but frozen during
geometry optimization at zero-T?


Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA