[gmx-users] Trjconv trouble

[Mark Abraham]

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
> <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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> 
> 
>