[gmx-users] Re: question about freeze

[Dr. Vitaly V. G. Chaban]

I think your RMSD of 0.000539742 is quite a small value, which can be,
at least theoretically, caused by the accumulation of errors. Can you
simulate your protein for a longer time to show that RMSD is indeed
significant?




On Sat, Jul 28, 2012 at 1:01 AM,
<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.
>
> 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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>
>



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