RE: AMBER: on the rst file of the current ruuning

From: Ross Walker <>
Date: Mon, 18 Sep 2006 08:58:01 -0700

Dear Fenghui,

> As your e-mail said, if we input with sander ------ &,
> I can turn off my laptop and the cluster will run it.
> One thing I cannot understand is that when I turn off
> my laptop, there will be a *.rst file of the current
> running of the current MD. When I recheck my sanser
> after sometine, does the cluster give my laptop
> another another*.rst of the current ruuning to replace
> the one the computer saved before I turned off the
> laptop? In my opinion, the *.rst should shows the most
> recent MD status, however how does the *.rst in my
> working directory reflect this?
> As we know, after we finish the current MD we can use
> *.rst to get the latest PDB file.

This shows a fundamental misunderstanding of the way cluster based computing
and networked filesystems work. I suggest you take the time to read up on
the basics of clusters and remote filesystems.

Without knowing how your cluster is setup and where the files are written /
how jobs are submitted etc etc it is very hard to even understand what your
email above is asking let alone how to answer it.

I suspect that your laptop just mounts a remote file system on the cluster
over the network and you are just remotely connecting to this filesystem.
Beyond this everything else would be just a guess.

Please speak to the person running your cluster and ask them for a quick 30
minute introduction to how things work.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Sep 20 2006 - 06:07:11 PDT
Custom Search