[gmx-users] Confusion in passing check point file
jalemkul at vt.edu
Thu Oct 11 15:40:41 CEST 2012
On 10/11/12 9:33 AM, Venkat Reddy wrote:
> Thanks Justin for the information. By the way, Could you please give me a
> hint on the release of new GPU-version (4.6)?
As I posted yesterday, I do not have any insight on a specific release date.
It's close, but I'm not involved in any of the remaining coding that's going on.
> 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,
>>> 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
>>> fine if I use directly the check point file generated during NPT-no PR
>>> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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