Re: DCD trajectories produced by SMD simulation

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Nov 15 2007 - 00:23:02 CST

On Thu, 15 Nov 2007, Peter Freddolino wrote:

> 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?

I have used SMD and Tcl forces with NAMD2.6 running on different
platforms and I never had that problem.

Regards,
Marcos.

>
> 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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