[gmx-users] Re: question about freeze

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

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.

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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