[gmx-users] Confusion in passing check point file

Venkat Reddy venkat4bt at gmail.com
Thu Oct 11 15:33:15 CEST 2012

Thanks Justin for the information. By the way, Could you please give me a
hint on the release of new GPU-version (4.6)?

On Thu, Oct 11, 2012 at 4:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 10/10/12 11:53 PM, Venkat Reddy wrote:
>> Dear all,
>> I am doing a protein-ligand simulation and following Justin's tutorials. I
>> have confusion in passing check point file to the next step in position
>> restrain simulation (during NPT). I am slowly releasing the restraints
>> during NPT simulation, *viz., 1000....100.....10....1....**noPR*. So,
>> during
>> NPT-PR, is it required to pass the check-point file generated in the
>> previous step to the next step (1000....100....10...1....**noPR)? or is
>> it
>> fine if I use directly the check point file generated during NPT-no PR
>> step
>> to final MD step?
> You seem to be asking two questions, so it's not really a matter of "or."
>  One should always pass the final checkpoint of the previous stage of
> simulation to the current stage.  So during your reduction of restraints,
> you should pass the checkpoint from the previous restraint strength.  At
> the outset of MD, you should pass the checkpoint from whatever the step
> immediately prior to it was, which, from the description, is NPT in the
> absence of restraints.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras

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