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

[Oliver Beckstein]

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/