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Constant pressure (fwd)
Sender: jay_banks@merck.com (Jay Banks)
Subject: WSN: Constant pressure
Anyone out there have experience with moderate-length (> 20 ps) MD
simulations of TIP3P water at constant pressure? When I run for 40 ps
or so, the volume seems to decrease monotonically. (Actually I think it
may be decreasing monotomically from the start, but gets really
noticeable after 20 ps: 1000-step averages of the box length for 125
waters are down in the low 14-Angstrom range, and overall average around
15.0, having started at 15.5; put another way, the average density for
the whole run is up to 0.035 molecules/A^3 from 0.033.) And the RDF's
averaged over the last 20 ps are very much flattened out. When I run
for ~25 ps (~5 ps heating & equil, 20 ps measurement), the RDF's over
the last 20 ps look reasonable.
Can anyone suggest a way around this? (I've already decreased the
compressibility parameter (in CHARMm) from 4.63e-5 to 1.0e-6, with no
apparent effect.) Or is 20 ps somehow an intrinsic limit to the
stability of this particular simulation?
Jay Banks