AMBER Archive (2009)

Subject: RE: [AMBER] binding free energy

From: Maryam Hamzehee (maryam_h_7860_at_yahoo.com)
Date: Mon Mar 02 2009 - 01:33:44 CST

Dear Don and Ross
Many thanks for your suggestions; It seems that there is enough space in my hard, I used the " df -h " command and here is the information about it:
 
Filesystem            Size  Used Avail Use% Mounted on
/dev/sdc1              69G   41G   25G  63% /
tmpfs                1012M     0 1012M   0% /dev/shm
/dev/sdb1             151G  189M  144G   1% /mnt/sdb1
/dev/sda1             151G  189M  144G   1% /mnt/sda1
 
I believe that the sudden pause of my simulation (using pmemd) is not related to disk filling up. If I want to continue my simulation, what I have to do, as I saied before, simulation has already done up to 8.4 ns, can I continue just as the 8.4 ns up to 20 ns.
 
 
Thanks in advance for your help,
Maryam

--- On Sun, 3/1/09, Ross Walker <ross_at_rosswalker.co.uk> wrote:

From: Ross Walker <ross_at_rosswalker.co.uk>
Subject: RE: [AMBER] binding free energy
To: "'AMBER Mailing List'" <amber_at_ambermd.org>
Date: Sunday, March 1, 2009, 8:59 PM

Hi Don,

> It would be nice if sander and pmemd would try to be a little more
> failsafe when writing the restrt file. For example, one could move
> the previous restrt file to a temporary location in the same directory
> (filesystem), write the new restrt, and then, if successful, delete
> the old. Of course, this would cause temporary spikes in disk usage
> that might make failure on a near-full filesystem come sooner rather
> than later. But I think it would be worth it to have failures from
> which one can recover more easily.

Amber 10 can already do something close to this. You just set ntwr<0 and
then every time it writes a restart file it will just append an increasing
number to the end of it. This way you can keep all restart files and you
avoid the problems of corruption happening during a restart write since you
don't overwrite previous restarts so only loose at most the time between
the
point of corruption and the previous restart write.

This of course does nothing to help you if you don't have the disk space to
store them all.

All the best
Ross

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|\oss Walker

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| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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