---------- Forwarded message ----------
Date: Fri, 23 Aug 2002 07:18:04 -0700 (PDT)
From: Pratul Agarwal <pratulka_at_rocketmail.com>
To: amber_at_heimdal.compchem.ucsf.edu
Subject: Re: Etot drops after restarting MD in sander
This email is for those of you who have asked me if I found the problem
(and for the archives).
Yes, I have found the problem. The problem was not with sander but with
my shell script for restarting the runs. In my script the file "refc"
was a symbolic link to restarting coordinates file. This is wrong, if
you have applied restraints, make sure that your "refc" file still
points to the original "refc".
--- Pratul Agarwal <pratulka_at_rocketmail.com> wrote:
> 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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Received on Mon Aug 26 2002 - 14:51:16 PDT
