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

[Oliver Beckstein]

> 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 ;-)).

> I also want to know how i can see the structure of my proteins/lipids in
> insight b'use insight is not reconize .xtc format, is there  any way to
> convert it in .pdb or any other suitable format.

Again, use trjconv. Alternatively, VMD can read xtc.

Oliver

-- 
Oliver Beckstein * oliver at biop.ox.ac.uk
 http://sansom.biop.ox.ac.uk/oliver/