[gmx-users] trjcat skipping frames

[Justin A. Lemkul]

Jared James Thompson wrote:
> The old information is given below. I haven't chopped into the code yet to see
> if Berk's fix is there.
> 
> http://www.mail-archive.com/gmx-users@gromacs.org/msg14689.html
> 

This error is unrelated to what you're doing.  The problem came with a 
combination of -b and -cat options to trjcat, neither of which you're using. 
The fix has been in place for some time, as noted in Berk's message 
(incorporated prior to the release of version 4.0).

If you want help with your specific problem, please answer the questions I posed 
before.

-Justin

> 
> ~j
> 
> 
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>>
>> Jared James Thompson wrote:
>>> Hi All,
>>>
>>> I'm having a problem with trjcat skipping frames. I saw a similar
>> complaint
>>> seemingly handled by Berk Hess in 2008. I wanted to know if his bug fix has
>> been
>>> incorporated into the current gromacs version.
>>>
>> Can you provide a link to this information?  What version of Gromacs are you
>>
>> using?  Presumably, if you're using the latest version, bugs from 2 years ago
>>
>> should be fixed.
>>
>>> I have a number of short .trj files of equal length and time spacing that I
>> want
>>> to cat together to form a single .trj file. I have a method for doing this
>> using
>>> trjcat and trjconv. It has worked normally in the past.
>>>
>>> The method is as follows. Set the start time of each trajectory to be the
>> next
>>> putative frame immediately following the previous trajectory, and also set
>> the
>>> timestep for each frame correctly, so for .trj of 10 frames long:
>>>
>>> trjconv -f frame_traj_2.trr -o ftc_2.trr -t0 20 -timestep 1.0
>>>
>>> trjconv -f frame_traj_3.trr -o ftc_3.trr -t0 30 -timestep 1.0
>>>
>>> etc.
>>>
>>> Once all the frame_traj_x files are together, then use trjcat to cat them.
>>>
>>> trjcat -f ftc* -o CombinedTraj.trj 
>>>
>>>
>>>  However, this time that I am using it, trjcat is producing the following
>>> response, note the timestep shown in the File Roster and that ftc_5 is
>> treated
>>> normally for some reason:
>>>
>>>          File                Start time       Time step
>>> ---------------------------------------------------------
>>>                 ftc_1.trr        0.000 ps        1.000 ps
>>>                 ftc_2.trr       20.000 ps        0.000 ps
>>>                 ftc_3.trr       40.000 ps        0.000 ps
>> Clearly something has broken down on a very fundamental level.  You set 
>> ftc_3.trr to have a start time of 30 ps above, but it has not worked.
>>
>> Some questions that may help diagnose your issue:
>>
>> 1. What is the spacing of frames in your original .trr files?
>> 2. What does gmxcheck tell you about each of your ftc_*.trr files?
>> 3. Does passing -t0 and -timestep to trjconv in separate steps make any
>> difference?
>>
>> -Justin
>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
> 
> 

-- 
========================================

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

========================================