[gmx-users] Combining position restraints with Parrinello-Rahman pressure coupling leads to instabilities

[Justin Lemkul]

On 8/21/18 2:32 AM, Naba wrote:
> Dear Dr. Justin,
>
> Thanks a lot for suggestions and hints.
>
> I issued:
>
> gmx dump -s npt.tpr
>
> to check the velocities.
>
> Following are last few lines after execution of the above command:
>
>     v[120488]={-8.24012e-01, -3.10189e-01,  3.53090e-01}
>     v[120489]={-5.70083e-02,  6.79958e-01,  1.43155e+00}
>     v[120490]={ 4.60961e-01,  8.73407e-02, -1.26087e+00}
>     v[120491]={ 3.43934e-01, -3.55264e-02,  5.41598e-02}
>     v[120492]={-2.71835e-01,  2.20839e-01, -2.95827e-01}
>     v[120493]={ 5.59665e-02,  6.66364e-01, -2.97680e-01}
>     v[120494]={ 1.22493e-01,  5.81446e-01,  1.32195e-01}
> Group statistics
> T-Coupling  :   33740  86755  (total 120495 atoms)
> Energy Mon. :   120495  (total 120495 atoms)
> Acceleration:   120495  (total 120495 atoms)
> Freeze      :   120495  (total 120495 atoms)
> User1       :   120495  (total 120495 atoms)
> User2       :   120495  (total 120495 atoms)
> VCM         :   33740  86755  (total 120495 atoms)
> Compressed X:   120495  (total 120495 atoms)
> Or. Res. Fit:   120495  (total 120495 atoms)
> QMMM        :   120495  (total 120495 atoms)
>                                     -----
>
> Using -maxwarn 1 in grompp, I produced the tpr file for Berendsen barostate
> also and got the same output. So, I can proceed with Berendsen pressure
> coupling, am I right?

If you're continuing from a previous state, you will naturally have the 
same velocities.

You should be able to proceed with a sensible equilibration.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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