Re: DCD trajectories produced by SMD simulation

From: Vlad Cojocaru (
Date: Tue Nov 13 2007 - 04:05:14 CST

Dear Peter,

I am running on our internal x86_64 Linux cluster (2*Dual Core AMD
opteron 2218, 4 procs per node, each proc 2600 Mhz), on 4 (1 node) or 8
procs (2 nodes).
The NAMD version is: NAMD_2.6_Linux-amd64-TCP

There is absolutely no error message (maybe next run I could run it with
strace and see if I can find out more) ... The job looks as if it
finished normally ... All output is complete (well except for the dcd
file) ....

The problem appears either with SMD or TclForces enabled and it is
independent on whether the job runs on 1 node or on 2 different nodes
.. The problem doesnt appear neither with standard simulations, nor
with ABF simulations.

It is not a dramatic issue since the .bak file is OK but I was just
wondering whether anybody else noticed such a problem ...


Peter Freddolino wrote:

>Hi Vlad,
>I certainly have not noticed this behavior in any of the SMD
>trajectories that I've run recently. Could you give a little more
>information on where you're running? Also, could you check whether your
>jobs are ending in the middle of a write to the dcd? The dcd.bak file
>should just contain the same information as the dcd from the previous
>Vlad Cojocaru wrote:
>>Dear NAMD community,
>>I noticed that the DCD trajectories produced by SMD simulation in NAMD
>>2.6 are corrupted (they cannot be loaded properly in VMD 1.8.6).
>>Luckily, NAMD creates also a DCD.BAK backup which can be properly
>>visualized. This problem is independednt of the trajectory size.
>>Is there a fix for this problem ?
>>Best wishes

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter

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