Re: Missing cphrst file

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon May 07 2018 - 08:36:38 CDT

I think you found a bug - most of the constant-pH testing just printed the
restart file at the end of the trajectory, so this must have been missed.
I'll work on a fix today.

That being said, a successfully completed trajectory absolutely should
print a cphrst file - are there any temporary files left in the working
directory (by default these start with the prefix, "namdcph")?

The restart file is just a simple JSON format file and can indeed be
recapitulated from the cphlog file, albeit arduously, especially for large
systems. It is also possible to simply start again without a restart if you
are just looking for quick equilibration. Contact me offline if you want to
consider doing this.

Brian

On Mon, May 7, 2018 at 8:59 AM, Yasser Bruno Ruiz Blanco <
ybruizblanco_at_gmail.com> wrote:

> Dears,
>
> I am using NAMD 2.12 to run constant pH simulations.
>
> Apparently everything run nicely OK except for the fact that the cphrst
> file is not saved during the run.
>
> I have used the following keyword expecting to obtain a *.cphrst file
> after every cycle:
>
> cphRestartFreq 1
>
> All other files are saved without problem.
>
> Is there a way to build this files afterwards, with the information in the
> cphlog file?
>
> Which is the format of this file?
>
> Should this be relevant, I am runing NAMD on a HPC system type OmniPath
> (OPA). I needed to compile NAMD form source code. So far I have use this
> compilation for regular MD, ABF and metadynamics without problems.
>
> Thanks!
>

This archive was generated by hypermail 2.1.6 : Sat Dec 14 2019 - 23:19:48 CST