Hi,
I am running MD simulations of a protein with Generalized Born conditions
(i.e. no periodic simulation, no water). Unfortunately, my system has
picked up quite some rotation (around center of mass) during the
equilibration.
This rotational motion is not removed with the nscm option (I tried
intervalls as small as 0.1 ps). How can I deal with this problem?
Here is the input file:
&cntrl
imin=0,
irest=1, ntx=5,
nstlim=125000, dt=0.002,
nscm=50,
igb=1, ntb=0, gbsa=1,
cut=15.0,
ntt=1, tautp=5.,
tempi=300., temp0=300.,
ntc=2, tol=0.000001,
ntpr=25, ntwr=5000, ntwx=250, ntwv=250,
&end
Thanks for any suggestions!
Have a nice weekend.
Raik
=====================================================
Raik Gruenberg | EMBL
| Meyerhofstr. 1
gruenber_at_embl-heidelberg.de | D-69117 Heidelberg
Tel: +49/62 21/38 72 96 | Germany
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Received on Fri Dec 01 2000 - 09:43:42 PST
