[gmx-users] Trjconv trouble

[Tsjerk Wassenaar]

Hi Guy,

Which version are you using? It may be there's a flaw in the code. If
you want the forces in human readable format, you can also try
converting the .trr to .g96

Hope it helps,

Tsjerk

On Mon, Sep 28, 2009 at 9:59 PM, Vigers, Guy
<Guy.Vigers at arraybiopharma.com> wrote:
> Dear Gromacs users,
>
>
>
>     I seem to be having trouble with trjconv.  I have run a short simulation
> and want to write out a trajectory with positions and forces.  However, when
> using trjconv to write out the trajectory I get the same result whether I
> try and write out velocities or forces:
>
>
>
>> mpirun -np 2 mdrun -np 2 -v -deffnm pr1
>
>> trjconv -f pr1.trr -s pr1.tpr -force -b 30 -e 40 -o test1.gro
>
>> trjconv -f pr1.trr -s pr1.tpr -vel -b 30 -e 40 -o test2.gro
>
>
>
>> head -5 test1.gro
>
> Generated by trjconv : Protein in water t=  30.00000
>
> 61767
>
>   331SOL     OW    1   0.745   1.223   1.235 -0.8542  0.4057 -0.0772
>
>   331SOL    HW1    2   0.662   1.257   1.197 -0.0011  2.1431 -1.5672
>
>   331SOL    HW2    3   0.803   1.297   1.208  1.5836 -1.7723 -2.4831
>
>
>
>> head -5 test2.gro
>
> Generated by trjconv : Protein in water t=  30.00000
>
> 61767
>
>   331SOL     OW    1   0.745   1.223   1.235 -0.8542  0.4057 -0.0772
>
>   331SOL    HW1    2   0.662   1.257   1.197 -0.0011  2.1431 -1.5672
>
>   331SOL    HW2    3   0.803   1.297   1.208  1.5836 -1.7723 -2.4831
>
>
>
>
>
> Here are the relevant lines from my .mdp file:
>
>
>
> ; ** Options for Output Control **
>
> nstxout                 = 100
>
> nstvout                 = 100
>
> nstfout                 = 100
>
> ;    Output freq for energies to log and energy files
>
> nstlog                  = 100
>
> nstenergy               = 100
>
> ;
>
>
>
> I get equivalent results whether I do all or part of the trajectory and
> whether I write out the whole system or just one part.  As you can see from
> the .mdp file, I am using the same output frequencies for everything.  I am
> running Gromacs 4.0.5
>
>
>
> Can anyone tell me what I'm doing wrong?  I apologize if it is a boneheaded
> error.
>
>
>
> Thank you in advance
>
>
>
> Guy Vigers
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623