AMBER Archive (2003)

Subject: AMBER: restart MD program

From: Do Anh Tuan (datuan_at_hcmuns.edu.vn)
Date: Wed Nov 26 2003 - 11:12:50 CST

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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