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

Alok alokjain at iitk.ac.in
Mon Sep 13 11:59:05 CEST 2004


Thanks for ur reply. now its genrating the .xtc file.
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???
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.

> Hi Alok,
>>  I was trying to genrate .gro (output which only contain coordinates
>> i.e. dppc128out.gro) and .xtc(dppc128.xtc) file but these file are
>> not genrating . or there is any other way to genrate a file which
>> contain only coordinates not other outputs(like velocity,energy
>> etc..).
> Have a look at the syntax for the mdp file,
> http://www.gromacs.org/documentation/reference_3.2/online/mdp_opt.html#out
> In order to write an xtc file you will want to set in your dppc128.mdp
> file
> nstxtcout = 500      ; if your timestep is 2fs this will write
>                      ; a frame every 1ps to the xtc file
> xtc_precision = 1000 ; precision is 0.001 nm (good value, keep)
> I also suggest you don't write to the trr file too often as it fills
> up disks quickly, eg
> nstxout = 50000      ; write coords and
> nstvout = 50000      ; and velocities every 100 ps
> nstfout = 0          ; and don't write forces
> Then you will still be able to restart every 100ps in case your
> simulation crashes.
>> my input for mdrun is as follows (dppc128 is my file name)
>> mdrun -v -s dppc128 -e dppc128 -o dppc128 -c dppc128out -x dppc128 -g
>> dppc128 >& dppc128.job &
> A gro file with final coords and velocities is automatically written
> at the end or when you kill gromacs with USR1, ie 'kill -USR1
> process_id'.
> Oliver
> --
> Oliver Beckstein * oliver at biop.ox.ac.uk
>  http://sansom.biop.ox.ac.uk/oliver/
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