[gmx-users] Problem in mdrun (writing xtc files)

[Anton Feenstra]

Oliver Beckstein wrote:

>>but it is genrating the dppc128out.gro only when my job is complete and
>>not if i kill my job (by using kill -USR1 or by kill -9 ) in between. so
>>what is the resone can u tell me???
> 
> 
> If it doesn't generate the gro file then you can always extract the last 
> frame of your trr (if you need high precision and velocities) or of your 
> xtc using trjconv (see trjconv -h, but something like trjconv -f in.xtc 
> -o  out.pdb -b 2000 -e 2000, where I assume that the last frame is at 
> t=2000ps, might do the job. Just try different options ;-)).

trjconv -f in.xtc -o out.pdb -dump 2000

will write the first frame with t>=2000 to out.pdb
You can use gmxcheck to see what is the last (whole) frame in your trajectory.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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