[gmx-users] Trjconv trouble

[Vigers, Guy]

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?

	Thanks again,

	Guy Vigers


-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] 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 
> <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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>>
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> 
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