AMBER Archive (2002)

Subject: Etot drops after restarting MD in sander

From: Pratul Agarwal (pratulka_at_rocketmail.com)
Date: Fri Aug 16 2002 - 13:18:58 CDT

This problem was posted about 2 weeks ago by someone else as well,
however, I do not see any "fix" in that e-mail thread.

Problem: After the MD run is restarted under AMBER 7.0, the total
energy (Etot) shows a drop after each restart. The energy plot looks
like a downward stair-case.

I have tried running a comparison with a single run and a sequence of
restart with total steps same as the single run. The single run shows a
fairly stable Etot while the restart drops the Etot by about 10
kcal/mol for each restart in my case.

I am using the following sander control files:

--- Single run ------
  &cntrl
   imin=0, irest=0, ntx=1,
   ntt=0, tempi=300.0 temp0=300.0, tautp=1.0,
   ntb=1, ntc=2, ntf=2,
   nsnb=10,
   nstlim=2000, t=0.0, dt=0.002,
   ntwe=1, ntpr=1, ntwx=10,
   cut=10.0, nscm=5000,
   ntwprt=6021,
 &end
---------------------

--- Restart ---------
 &cntrl
   imin=0, irest=1, ntx=5,
   ntt=0,
   ntb=1, ntc=2, ntf=2,
   nsnb=10,
   nstlim=500, dt=0.002,
   ntwe=1, ntpr=1, ntwx=10,
   cut=10.0, nscm=5000,
   ntwprt=6021,
 &end
----------------------

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