[gmx-users] Trjconv trouble
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Oct 1 00:58:24 CEST 2009
Vigers, Guy wrote:
> 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?
Not as far as I know. Easier perhaps would be to do the one-liner change
to your 4.0.5 source, viz:
commit bb50c6a370e653c973cf8f5f8876e526fa5e7e84
Author: Berk Hess <hess at csbl10.cbr.su.se>
Date: Wed Sep 16 18:30:21 2009 +0200
fixed setting of bF boolean in trxframe
diff --git a/src/gmxlib/trxio.c b/src/gmxlib/trxio.c
index 28e1d59..6dcdfc4 100644
--- a/src/gmxlib/trxio.c
+++ b/src/gmxlib/trxio.c
@@ -388,7 +388,7 @@ static bool gmx_next_frame(int status,t_trxframe *fr)
if (fr->flags & (TRX_READ_F | TRX_NEED_F)) {
if (fr->f==NULL)
snew(fr->f,sh.natoms);
- fr->bF = sh.f_size;
+ fr->bF = sh.f_size>0;
}
if (fread_htrn(status,&sh,fr->box,fr->x,fr->v,fr->f))
bRet = TRUE;
So changing line 388 of src/gmxlib/trxio.c to be "fr->bF = sh.f_size>0;"
and recompiling should solve the issue. It might not be line 388 if
there have been other changes since your version of GROMACS was
released, but you should be able to recognize the right line from the
context given above.
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: 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
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
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