AMBER Archive (2004)

Subject: AMBER: question about production runs

From: opitz_at_che.udel.edu
Date: Fri Jul 16 2004 - 14:42:06 CDT

('binary' encoding is not supported, stored as-is) Dear Amber Community,

I had a general question about production runs. I am using Amber7.
Once the system has equilibrated in a periodic box, what do I with the
file. After a few picoseconds of equilibration, the system is relatively
stable and the values such as density and Volume of the box are fairly
constant. But they do still change? Are they allowed to change during the
production run? I've heard that you should pick the density you want and
run that, but how would I do that in Amber? Or do I just run the system
with the box volume being able to change? I will include an input file
to see if those settings would be accetable for a production run.
Thanks in advance,

Armin

&cntrl
 imin=0,
 irest=1,
 ntx=5,
 ntb=2,
 pres0=1.013,
 ntp=1,
 taup=2.0,
 cut=12,
 ntr=0,
 ntf=1,
 ntt=1,
 iwrap=1,
 tempi=300.0, temp0=300.0, tautp=1.0,
 nstlim=200000, dt=0.001, t=300,
 ntpr=100, ntwx=100, ntwr=1000
&end

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