Hi David,
Thank you for your answer. I'm still unclear about a few points.
I understand that I can manually input the box dimensions. But what value should I use after equilibration in NPT? I ran my system for 5ns using NPT. Will the value back calculated from the last 1ns suffice? Also, does it make sense that the density of my system increases by 1% over 5ns of equilibration? Or does it mean that my system hasn't reached equilibrium yet?
Thank you for the trick, that is very helpful.
Best regards,
Quynh Vo
On Thursday, April 24, 2014 12:31 PM, David A Case <case.biomaps.rutgers.edu> wrote:
On Thu, Apr 24, 2014, Quynh Vo wrote:
>
> My question is that when I make the switch, what volume information will
> be used by amber for the constant volume? Is it the volume that was
> last written out to the restart file?
Yes.
> If that is the case, then what
> will happen to the density of my system, as during NPT
run, the density
> fluctuated with volume.
> Or my concern would be dismissed if the last volume that is written out
> to the restart file is the average volume over the whole equilibration.
You can manually edit the restart file to put in whatever box dimensions you
want, e.g the average over the last N steps of the NTP run. One would
generally not want the average over the whole equilibration.
One "trick" that we often use: set ntp=1, but taup=9999999. This will allow
you to monitor
the pressure during what is still a constant volume run.
...dac
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Received on Thu Apr 24 2014 - 13:30:08 PDT
