Re: Is the DCD file size consistent for consecutive runs?

From: Bjoern Olausson (
Date: Fri Oct 08 2010 - 11:30:36 CDT

On Friday 08 October 2010 16:07:08 you wrote:
> I've used the dumpdcd.c program in the NAMD src directory to look at the
> headers of the truncated files. The two dcd files I've looked at
> (npgt322.dcd and npgt232.dcd) appear to have been processed by some
> program that claims to be CHARMM 34, but NAMD pretends to be CHARMM 24.
> Do you have the original dcd files output by NAMD?
> -Jim
Well, the setup and the PSF, PSF.EXPLOR, and PDB files were generated with
CHARMM 34b2. But the all runs where run with namd 2.7b2 Linux-x86_64-net-

I just did some analysis with CHARMM but only opened the dcd files for
reading. I never did changes to the original files produced by NAMD.

To answer you second question:
> If that is the pattern then you should be able to reproduce the truncation
> effect by repeating an earlier run. Have you tried this?
I restarted from run051 and run052 successfully completed. Same for the other
broken files.

I am kind worried that it really will re occur at run412.

Thanks for your help.

Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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