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.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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Received on Wed Nov 26 2003 - 17:53:01 PST
