AMBER Archive (2009)
Subject: [AMBER] Equilibrium water density
From: Myeong Lee (myeong.lee_at_nano.tu-dresden.de)
Date: Wed Jul 15 2009 - 03:58:52 CDT
I tried to equilibrate my system with constant pressure, but found the
following error after 174 ps. I first heat the system from 0 K to 300 K
for 20 ps, and tried to equilibrate water density for 500 ps with
vlimit exceeded for step 87428; vmax = 40.2588
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 3 366 1181 1183
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
But, when I checked the energy, temperature, density and volume,
everything looked fine at least until it dies. Does anyone have this
kind of error?
Also, I'm wondering how long the equilibrium should be done. The
density was 0.9991 g/cm^3 before it was killed.
One more thing, I didn't give restraint for the molecule (dna) while I
give constant pressure (although I gave restraint during heating) as
Amber tutorial says. Is this the right way to do?
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