equilibration of solvent box and pressure

From: Hiroaki Maekawa (hmaekawa_at_uci.edu)
Date: Sun Oct 05 2008 - 22:10:49 CDT

Dear NAMD users,

I'm trying to equilibrate a CHCl3 box with 1060 molecules.
After about 2 ns NPT run, the average pressure is slightly off (1.2-1.3)
from the target
value of 1.013 bar, though the temperature is regulated well (293 K).

Let me ask several questions on this.
1) Do I need to plot PRESSURE or PRESSAVG?
I just wonder the latter is the average between energy outputs according
to the manual,
but the number of printed data is same for PRESSURE and PRESSAVG.
Why is it?
Is it true that the PRESSURE value doesn't make any sense if multi time
step is
used to calculate different forces?
If this is the case, PRESSAVG, which is the average of PRESSURE, also
seems to be

In addition, is it better to take average of all of 2 ns data or just
final 500 ps is enough
to check whether the average pressure is close to the target value?

2) Does just a much longer simulation lead to the average value or
is there any good technique to shorten the equilibration time?
I just would like to know how long the equilibration needs to be
continued usually.

Thank you for your answers.



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