[gmx-users] Re: trjconv help

[Mark Abraham]

sarbani chattopadhyay wrote:
>   hi,
>     I had run MD simulations where the output control parameters were
>    
>     nstxout=250
>     nstvout= 1000
>     nstenergy=100
> Due to this the '.trr' file is very large. I want to compress this file 
> so that
>   xyz coordinates are stored every 1000 steps,
>   velocity is stored every 250000 steps and
>   energy every 1000 steps.

The usual way to do this kind of thing is with nstxtcout < nstenergy < 
nstvout = nstxout. See 
http://wiki.gromacs.org/index.php/Using_Trajectory_Information

>   The timestep is .002ps.
> I will have to use the 'trjconv' file,but will it be possible to do it 
> in one single command as
> the frequency of storing the xyz coordinates,velocity and energy are 
> different,
> I think Compressing the files using 'skip' will not be of much help .

There are options to trjconv that will be useful for suppressing output 
of velocities and/or forces, see trjconv -h. Anyway, you will not be 
able to do this operation in one invocation of trjconv, and you will not 
end up with a single trajectory either.

Mark