[gmx-users] Combining energy files

[Martin Kamp Jensen]

On Wed, Sep 28, 2011 at 1:33 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 28/09/2011 9:11 AM, Martin Kamp Jensen wrote:
>
> On Tue, Sep 27, 2011 at 3:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> Martin Kamp Jensen wrote:
>>
>>> Hello,
>>>
>>> I need to combine several trajectories (.xtc) and energy file (.edr)
>>> pairs. In the end I need all the conformations of the trajectories and a
>>> specific energy value for each of them.
>>>
>>> To combine two trajectories, I use trjcat [1] like this:
>>>
>>>    trjcat -f first.xtc second.xtc -o combined.xtc -cat
>>>
>>>
>>> Since I just need the conformations (the coordinates) and I do not care
>>> about "step" and "time," I guess this is okay.
>>>
>>> To combine two energy files, it seems like I should use eneconv [2].
>>> Unfortunately, there is not an argument like "-cat" for trjcat, which means
>>> that the tool will not include all energies from the input files in the
>>> output file ("In case of double time frames the one in the later file is
>>> used."). I should probably note that I do not need "Av. Energy" or "Sum
>>> Energy," I just need the energy frames in the energy files concatenated so
>>> that I can easily extract them and assign them to the correct conformations.
>>>
>>> Any ideas?
>>>
>>>
>>  Don't use the -cat option of trjcat.  Normally you'll have duplicate time
>> frames, for instance, in the final frame of "first.xtc" and the first frame
>> of "second.xtc."  If they are the same, you do not need to keep them.  The
>> -cat option, as I understand it, is basically for fudging different
>> trajectories together for non-standard purposes.  If you omit -cat then
>> you'll have .edr and .xtc files that match.
>>
>
>  But my purposes are non-standard and I need all of the conformations of
> both (or more) input trajectories as well as the corresponding energy
> frames. I see that, per the description of "-cat," time and step information
> will be messed up, but that is not a problem.
>
>
> So pre-process with -settime such that duplicate times cannot arise.
>

Ah, thanks!


>
> Mark
>
>
>
>  (I have created a program that reads conformations from a trajectory and
> assigns a specific energy value from a corresponding energy file to each of
> the conformations. I just had a special case where I was asked to work with
> several trajectories and energy files which were provided to me and it would
> be nice to just concatenate them and then not introduce special
> functionality in my program to handle it.)
>
>
>>
>> -Justin
>>
>>
>>  Regards,
>>> Martin.
>>>
>>> [1] http://manual.gromacs.org/online/trjcat.html
>>> [2] http://manual.gromacs.org/online/eneconv.html
>>>
>>>
>>  --
>> ========================================
>>
>> 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
>>
>> ========================================
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>
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