AMBER Archive (2003)

Subject: nasty npt md problem (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Wed Mar 05 2003 - 12:05:58 CST

---------- Forwarded message ----------
Date: Wed, 5 Mar 2003 11:54:19 +0100 (MET)
From: seraphimo_at_gmx.de
To: amber_at_heimdal.compchem.ucsf.edu
Subject: nasty npt md problem

hi everybody,

i have some deep troubles with my md simulations and wonder if somebody
could help.
the system i prepared is a polymer under pbc plus a tip3 water molecule in
order
to study diffusion behaviour. anyway, while i'm doing nvt md everything
works fine.
when i switch to npt md then there is a raise in density at a certain point
followed by
a drop and the simulation stops for ewald bomb reasons. obviously there is
some vlimit
exception. i used different cutoffs, different timesteps, shake ntc=3,
annealed for
more than two nanoseconds, minimized several times and always run into this
problem.
i attache my mdin file and would be glad if somebody could give me a hint.

cheers, mike.

&ctrl
imin=0,
ntx=5,
ntb=2
irest=1,
iwrap=1,
ntwx=100,
ntave=100,
cut=7.0,
ntc=3,
jfastw=0,
nstlim=200000,
dt=0.001,
temp0=300,
tempi=300,
ntt=1,
pres0=1.0,
taup=1.0,
comp=28.0,
&end 

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