VMD-L Mailing List

From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Fri Dec 09 2016 - 10:17:47 CST

By default, NAMD only writes checkpoint files after regular termination. If
you use "restartFreq <freq>" then restart files will be re-written every
<freq> steps and you can recover a crashed run from the most recent one of
these. Some things to consider:

1) Having a small value for restartFreq can dramatically reduce performance
2) You have to be mindful of redundant output to DCD and stdout whenever
DCDFreq and/our outputEnergies is smaller than restartFreq (which is almost
always the case)
3) I don't use this option a lot, but if memory serves, restartFreq causes
*two* sets of restart files to be written, since the normal termination
output goes to [outputname].coor/.vel/.xsc, whereas the "new" restart
output goes to [outputname].restart.coor/.vel/.xsc

HTH,
Brian

On Fri, Dec 9, 2016 at 8:25 AM, Naeem Mahmood Ashraf <
naeem.mahmood_at_uog.edu.pk> wrote:

> Hi Everyone,
>
> We are using command line interface for NAMD and there are some issues
> that we are facing regarding the software.
> How can be checkpoints produced in NAMD for restoring simulation if the
> system restores/restarts or crashes from any reason?
> Is there a specified command for the creation of random checkpoints that
> are to be added in the configuration file?
> Can we add directed checkpoints in the scripted configuration file and if
> yes then what could be the possible command for that?
>
> --
> *Naeem Mahmood Ashraf*
> *Lecturer Biochemistry & Molecular Biology *
> *University of Gujrat, Punjab *
> *Cell Number: +923355064805 <+92%20335%205064805>*
> *E-mail: naeem.mahmood_at_uog.edu.pk <naeem.mahmood_at_uog.edu.pk> *
> 

-- 
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov