Vigers, Guy wrote:
Dear GMX-users
Thank you for your suggestions on trjconv. I am using Gromacs 4.0.5.
I have done some more troubleshooting, as suggested, and here are the
results:
On a very short md run (just 500 steps), gmxcheck shows that the .trr
file does contain force as well as velocity data:
gmxcheck -f pr2.trr
Item #frames Timestep (ps)
Step 6 0.1
Time 6 0.1
Lambda 6 0.1
Coords 6 0.1
Velocities 6 0.1
Forces 6 0.1
Box 6 0.1
Similarly, gmxdump gives data lines for position, velocity and force.
However, no matter how I use trjconv, I always lose the force data. For
instance:
trjconv -f pr2.trr -s pr2.tpr -force -o test3.xtc
gmxcheck -f test3.xtc
Item #frames Timestep (ps)
Step 6 0.1
Time 6 0.1
Lambda 0
Coords 6 0.1
Velocities 0
Forces 0
Box 6 0.1
Or, if I do:
trjconv -f pr2.trr -s pr2.tpr -force -o test3.g96
test3.g96 has data for POSITIONRED and VELOCITYRED, but not for force.
So, at the moment it looks to me like a bug in trjconv.
In the worst case I can access the forces through gmxdump, but does
anyone have any other suggestions? Is there an older version of trconv
which is known to export forces correctly?
There is a known bug with reading forces from trajectories that has been
fixed for future GROMACS releases. You could try getting the development
source via git; the release-4-0-patches branch version of trjconv should
no longer show this bug.
Mark
Thanks again,
Guy Vigers
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Mark Abraham
Sent: Monday, September 28, 2009 11:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Trjconv trouble
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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any disclosure, copying, distribution or use of the contents of this
information is prohibited. Please notify the sender of the delivery
error by replying to this message, or notify us by telephone
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