Re: [AMBER] how can i run as one sander job?

From: Ross Walker <>
Date: Wed, 16 Jun 2010 02:49:41 -0700

Hi Vaibhav,

> Actually we have amber10 installed on a HPC cluster where we can access
> it
> only through a portal which allows to submit only sander jobs. So I'm
> looking for a method to link all the sander (min, heat, density and
> equil)
> jobs in one sander input where I can give initial prmtop and inpcrd
> files
> and the jobs can run sequentially.
> Please find time and see if you can suggest some solution to the same.

This functionality does not exist and would need a substantial amount of
code changes to the main code to be able to achieve this. You could write
yourself a little wrapper program in c or fortran that uses system calls to
execute one or more sander / pmemd jobs etc in serial of parallel as needed.
This is effectively an overly complex shell script. I use these a lot to
circumvent overly restrictive HPC queuing systems but in your case it sounds
like things are locked down far too tight. E.g. you'd have to hack the
portal to let you submit your wrapper program in place of the sander job.

Your best bet is probably just to keep phoning the admin for the machine
until they get fed up enough to give you a real login.

Good luck,


|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

AMBER mailing list
Received on Wed Jun 16 2010 - 03:00:06 PDT
Custom Search