Tsjerk Wassenaar wrote:
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
Moreover you can see if they exist in the .trr file by using gmxdump.
Mark
On Mon, Sep 28, 2009 at 9:59 PM, Vigers, Guy
<[email protected]> 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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