[gmx-users] gmxcheck and trjconv

[andrea spitaleri]

Hi
nope they are both finished. I have also checked the edr files and the time does not correspond to
the time found in the respectively trr files. Those MD are carried out in a supercomputer (SARA in
Amsterdam) and they were killed by the queue system. Probably as you said a buffer problem ...

gmx version 3.3.1

Regards

andrea

David van der Spoel wrote:
> andrea spitaleri wrote:
>> Hi all,
>> silly question. I have checked a trr with gmxcheck and I get this
>> output below:
>> Item        #frames Timestep (ps)
>> Step            70    1
>> Time            70    1
>> Lambda          70    1
>> Coords          70    1
>> Velocities      24    3
>> Forces           0
>> Box             70    1
>>
>> however if then i use trjconv to dump a configuration file at 70 ps it
>> says:
>> WARNING no output, trajectory ended at 69
>>
>> Is it normal? I don't mind to extract a configuration file at 69 ps,
>> however i was wondering if this
>> behaviour is normal or whether it is bug.
>>
>> thanks in advance
>>
>> Regards
>>
>> andrea
> is the simulation still running? then file buffering may play in. alt.
> if you kill -9 then the buffers will not be flushed.
> 

-- 
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------