Re: DCD trajectories produced by SMD simulation

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Nov 15 2007 - 07:49:58 CST

Hi Peter,

I think I need to applogise about this .... I really hope you didnt
spend too much time on it .... In my scripts I assigned by mistake the
same name to the velocity .dcd file and the coordinates .dcd file
..Therefore, the .dcd file contains velocities while the .dcd.bak
contains coordinates ....

I was running many different simulations, I built a script which was
changing parameters and producing different trajectories and since I
always got a trajectory (.dcd.bak) I concentrated on the results .. I
didnt check anymore that part of the script assigning output file names
... ...

I am sorry for taking your time on this .....

Well, actually its very nice that NAMD still produced this .dcd.bak file
... Otherwise I wouldnt have had the trajectories .... (on the other
hand I would have noticed the mistake earlier ;-) )

Sorry ....

Best
vlad

Peter Freddolino wrote:

>Hi Vlad,
>could you try using catdcd on one of the corrupted dcds to see whether
>the whole file is corrupted or just the last frame? It should throw an
>error if you're reading bad sections of the file, so by specifying -last
>to be one before the end you can see where problems occurred. I haven't
>been able to reproduce this on my setup, though... has anyone else on
>the list seen anything like this?
>
>Peter
>
>Vlad Cojocaru wrote:
>
>
>>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 ...
>>
>>Cheers
>>vlad
>>
>>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
>>>timestep...
>>>
>>>Best,
>>>Peter
>>>
>>>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 ?
>>>>
>>>>Thanks
>>>>
>>>>Best wishes
>>>>vlad
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>
>
>

-- 
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Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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