VMD-L Mailing List

From: Chandra Ramananjara (mozart20d_at_yahoo.com)
Date: Tue Aug 05 2008 - 18:49:40 CDT

Hi Peter,
Thanks for the suggestion. I will download the vmd-1.8.7 version of NAMDENERGY.

-Chandra

--- On Tue, 8/5/08, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
From: Peter Freddolino <petefred_at_ks.uiuc.edu>
Subject: Re: vmd-l: NAMDENERGY crashing repeatedly
To: mozart20d_at_yahoo.com
Cc: "VMD Mailing List" <vmd-l_at_ks.uiuc.edu>
Date: Tuesday, August 5, 2008, 5:26 PM

Hi Chandra,
I'll try hammering on this and see if I can reproduce your problem. In
the meantime, however, you may want to try the vmd 1.8.7 beta available
on biocore, which has a -updatesel flag to automatically update the
selection between frames.
Best,
Peter

Chandra
 Ramananjara wrote:
> Hi all,
> I am writing to report a problem I'm having with NAMDENERGY. I am
> using NAMDENERGY to calculate interaction energies in every frame of a
> trajectory I have. Since the interacting atoms (between which energies
> are calculated) are different for each frame, I have to run NAMDENERGY
> once for each frame, so over the course of my 12000 step trajectory,
> NAMDENERGY is repeatedly called 12000 times. I've noticed that
> sometimes it crashes and gives a strange error. This error is of the
> form:
>
> error deleting "namd-temp.*": no such file or directory,
>
> where "namd-temp.*" is any of the temporary files used by
NAMDENERGY
> (i.e. namd-temp.namd, namd-temp.dcd, namd-temp.pdb, namd-temp.log,
> etc.). There's no rhyme, reason, or pattern to this error, it occurs
> completely randomly, after running fine for
 hundreds or thousands of
> iterations. The files involved in the errors are also random, but it's

> always one of the namd-temp.* files.
>
> I've been trying to figure out how or why this error occurs and what
> makes it so difficult to figure out is that it occurs so randomly. My
> best reason for it is that I run NAMDENERGY too many times. Most
> people who use NAMDENERGY usually run it just once for a whole
> trajectory since the groups of atoms they're calculating energies
> between are the same for all frames of the trajectory. For my system,
> the interacting atom groups vary from frame to frame so I have to run
> NAMDENERGY once for each frame, instead of once for the whole
> trajectory. Has anyone encountered this error ?
>
> Thanks,
> Chandra
>
>