[gmx-users] Trjconv trouble
Vigers, Guy
Guy.Vigers at arraybiopharma.com
Wed Sep 30 23:28:28 CEST 2009
Hi Mark,
I believe that answers my question nicely. Thank you! Since I
am a bit leery of installing the patch version, I think that I might
just use the output from gmxdump for the moment. Are there any known
bugs in the gmxdump output?
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: Tuesday, September 29, 2009 6:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Trjconv trouble
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: 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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