AMBER Archive (2009)

Subject: [AMBER] Restarting an MD Simulation

From: Hopkins, Robert (hopkins_at_uhcl.edu)
Date: Wed Feb 04 2009 - 18:34:16 CST

Amber Users,

 

I'm using AMBER9 to do some MD calculations and one of my runs was
stopped after NSTEP = 179000 because of a power glitch. The restart
file at this point was named IIL.rst. After reading about Weight
Change Information for NSTEP0 on p. 109 of the User's Manual, it
appeared that restarting the run with NSTEP=180000 and continuing to
NSTEP=250000 should be straightforward. So, I used the following mdin
file:

 

Continue dodecamer equilibration at 300K & P=const.; no DNA restraints;

                SHAKE on; MD on; from NSTEP 180000 to 250000.

 &cntrl

  imin = 0, irest = 1, ntx = 5,

  nstlim = 71000, dt = 0.002,

  ntc = 2, ntf = 2,

  cut = 8.0, ntb = 2, ntp = 1, taup = 2.0,

  ntpr = 1000, ntwx = 1000,

  ntt = 3, gamma_ln = 2.0,

  temp0 = 300.0, nmropt =1

 /

 &wt type='NSTEP0', istep1=179000 /

 &wt type='END' /

 

along with the command:

 

sander -O -i mdin -o IIL2.out -p IIL_sol.prmtop -c IIL.rst -r
IIL2.rst -x IIL2.mdcrd &

 

The MD calculation evidently proceeded as expected except that the
values of NSTEP began at 1000 and continued to 71000. I'd appreciate
any suggestions of what I need to do differently to correct this result.
Thanks.

 

Bob Hopkins

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