[gmx-users] Confusion in passing check point file

Justin Lemkul jalemkul at vt.edu
Thu Oct 11 12:50:12 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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