[gmx-users] Re: question about freeze

[Mark Abraham]

On 28/07/2012 3:01 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi,
> my problem is, that during the md run the atoms are not frozen somehow.
> During the minimization run everything worked out fine. But when I did a
> md run the hydrogen atoms and the other atoms seems to be changes somehow.
> I calculated the RMSD value and this is why I know that they change.
> After the minimization the RMSD value between the structure before and
> after the minimization was about 9.9515e-08 but after the md run the RMSD
> value was 0.000539742 nm which definitely shows that something was
> changed.
> And I want to now why that happened. Because I thought that with the
> freeze option the atoms which are frozen are not changed.

The most likely explanations are that you aren't comparing 
configurations that should be the same, or that you are comparing them 
over a different set of atoms than were frozen. But without seeing the 
commands and groups chosen in your workflow, nobody can know.

Mark

>
> Thank you
>
>>> 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
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>