AMBER Archive (2009)

Subject: RE: [AMBER] Using a restart file

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jan 15 2009 - 10:52:44 CST

Hi Simone,

> I have been running a MD using sander when my computer crashed.
> The commands I have been using are:
> Sander -I script4.in -o script4.out -p dp10.prmtop -c script3.res -r
> script4.res
>
> Is there any way of using the restart file to continue this run from where
> it stopped when the computer crashed?

Yes you can assuming you weren't unlucky enough to have the machine crash
while it was in the process of writing the restart file. If you check the
top of the restart file it should have the time printed for the point it
represents. E.g.:

 9560 0.2000000E+02
  42.4596293 35.9445430 20.4511672 42.1136446 35.5114287 21.2349445

The 0.2E02 here means this represents 200ps. This is actual time for the
total run, not just for the run that generated the restart file. You can
then look in your output file and locate this time and that will be the
point at which your calculation will restart.

You then build yourself a new input file that includes irest=1 and ntx=5 if
the current one doesn't have that, you might also need to adjust the number
of steps to exclude what has run so far (up to the time you found in the
restart file and previous output file) - you may also need to adjust any
step dependent scaling you might have, say NMR weight restraints on temp0
for example.

If this is a simple MD run though all you need to do is make sure your new
input file is setup for restarts with the irest=1 and ntx=5 flags, which it
may already be if this was a step in a series of runs that previously
involved heating, equilibration etc.

Then you just feed sander the restart file as the input coordinates. So if
you named your input file script4_res1.in then you would use for example

sander -O -i script4_res1.in -o script4_res1.out -p dp10.prmtop -c
script4.res -r script4_res1.res -x script4_res1.mdcrd

Good luck,
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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