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.
-Justin
On Thu, Oct 11, 2012 at 4:20 PM, Justin Lemkul <jalem...@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
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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