[gmx-users] Trjconv trouble

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 29 23:49:04 CEST 2009 

Instead of using trjconv, have you tried writing the forces using g_traj -of?

-Justin

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?
> 
> 	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
>>>
>>>
>>>
>>>
>>>
>>> (please ignore the boilerplate below:)
>>>
>>>
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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