On Wed, Jul 19, 2023, Zafar,Muhammad Saqlain wrote:
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>I am taking densityy after equilibration. The whole NPT run for 10ns and i
>took from range of 2ns-10ns.
>
>I get density from output file that generated from NPT of each time frame
>of 0.00005.
Look at (plot) the time dependence of the density: is it changing with time?
Is there any pattern to the fluctuations? It is very odd to see the density
fluctuations you reported in a previous email, and (as mentioned) the
average density is way off.
I would also recommend visualizing the trajectory (after using autoimage in
cpptraj). I'm still concerned that you say that your unit cell had was 30
Ang on each side, which is very far from what it should be.
We would probably need to get access to files that would enable the problem
to be replicated.
....dac
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Received on Wed Jul 19 2023 - 13:00:02 PDT
