AMBER Archive (2003)

Subject: Re: AMBER: restart MD program

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Nov 26 2003 - 11:23:06 CST

you won't need the trajectory file to restart. later you can use ptraj
to combine your mdcrd files from the original run and the restarted one.
your input file is already set up for restarting so it looks OK.
just make a new sander script where you change the input and output names.
use the old restart file name as the new input coordinate file.
I would use something like this (but you might do it differently):
SANDER -O -i md2.in -o md2.out -p ph.parm -c eq_long.rst -r md2.rst -x md2.crd

carlos
  ----- Original Message -----
  From: Do Anh Tuan
  To: amber_at_scripps.edu
  Sent: Wednesday, November 26, 2003 12:12 PM
  Subject: AMBER: restart MD program

  Dear amber users,
  I would like to run a MD simulation for few nanoseconds. But I don't know how to restart with the restrt (eq_long.rst) and mdcrd (eq_long.crd) files which are results of the previous MD simulation. Could somebody help me please? Thank you in advance.

  This is md.in file:
  -----------
  &cntrl
   imin=0,
   irest=1, ntx=7,
   iwrap=1,
   ntf=2, ntb=2,
   nstlim=1000000, dt=0.001,
   ntt=1, temp0=313.0, tautp=1.0,
   ntp=1, pres0=1.0, taup=1.2,
   ntc=2,
   ntpr=100, ntwx=2000, ntwr=1000,
  &end

  And sander command:
  ----------
  SANDER -O -i md.in -o eq_long.out -p ph.parm -c heat.rst -r eq_long.rst -x eq_long.crd

    D.A.Tuan
  Laboratory of Molecular Biotechnology
  University of Natural Sciences
  Vietnam National University - Ho Chi Minh City
  227 Nguyen Van Cu St., Dist. 5, HCM City, Vietnam

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