[gmx-users] Trjconv trouble

[Vigers, Guy]

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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