[gmx-users] question about freeze

[reisingere at rostlab.informatik.tu-muenchen.de]

HI everybody,

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


Are there any problems in this file? I don't see any problems.

Thank you,
Eva