AMBER Archive (2000)

Subject: removing rotation during MD

From: Raik Gruenberg (Raik.Gruenberg_at_embl-heidelberg.de)
Date: Fri Dec 01 2000 - 11:43:42 CST

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

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Raik Gruenberg | EMBL
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