AMBER Archive (2001)

Subject: Re: batch mode

From: Jake Isaacs (rjisaa0_at_pop.uky.edu)
Date: Mon Feb 12 2001 - 12:18:28 CST

>Hello,
>Can anyone let me know if it's possible to do simulations in batch using
>AMBER6.0?
>
>Thanks in advance
>
>
>
>Fernanda TAVARES CAMARINHA
>Laboratoire de Pharmacochimie Moléculaire
>Université D. Diderot - Paris 7
>2, place Jussieu
>75005 PARIS
>Tel: 33 (0) 1 44 27 60 60
>Email: camarinh_at_ccr.jussieu.fr
>

I like to equillibrate my systems by running a series of minimization and MD
simulations from one command file that has all the sander and command line
instructions all in one place (things in parentheses are replaced by your
instructions, commands, files, etc.). The "cat" command concatenates
everything after it into the file you specify until it encounters the string
you specify, "eof" and "eof2" in these cases.

cat << eof > min1.in
 (sander instructions you would put in an input file)
eof
sander -i min1.in ...(other files needed to run sander)
(processing perlscripts and other commands)
cat << eof2 > md1.in
 (sander instructions you would put in an input file)
eof2
sander -i md1.in ...(other files needed to run sander)
(processing perlscripts and other commands)

(continue for as many jobs as you want)

This way you can have all your input instructions, sander file
specifications, and processing script specifications in the same place and
all you have to do is change this command file to executable and run it! By
including other commands you would issue from the command line, you can
seperate information on each run into seperate directories for easy checking
after each job or all jobs have finished. Also, by queuing everything up
this way, the machine doesn't sit idle while waiting for you to check the
last job and start a new one.

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