AMBER Archive (2009)

Subject: RE: [AMBER] How to restart the umbrella sampling jobs?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Mar 03 2009 - 10:00:04 CST

Hi Catherine,

> I would like to restart the following calculations, while it clash
> accidentially.
>
> $AMBERHOME/exe/sander -0 -i x_md1.in -o x_md1.out -c x_md0.restrt -p
> x.prmtop -r x_md1.restrt -x x_md1.mdcrd
>
> In fact the job has already started, and 200 steps out of 500 steps has
> already finished.
>
> Can I restart the job so that the results of the missing 300 steps could
> be continuously written to x_md1.mdcrd and x_md1.result files?

Assuming a restart file was written at 200 steps (you will need to look at
the top of the restart file and see what the time is listed as) then you can
continue the calculation of the remaining 300 steps. You need to modify your
mdin file so it only runs 300 steps instead of 500. You also need to set
irest=1 and ntx=5 if you haven't already.

However, you cannot append to the existing files. You will need to run with
new mdout, mdcrd, and rst files etc. Giving the old rst file as the input
coordinates with -i. You can then use ptraj later to append the two mdcrd
files into one file if you want to.

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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