[gmx-users] trjconv_d

[Justin A. Lemkul]

Alessandro.Maiorana at roma2.infn.it wrote:
> I proved the following commands:
> 
> trjconv_d -f filename.trr -o newfile.trr -s struct.gro -pbc nojump
> trjconv_d -f filename.trr -o newfile.trr -s struct.gro -fit rot+trans
> trjconv_d -f filename.trr -o newfile.trr -s struct.gro -pbc whole -center
> trjconv_d -f filename.trr -o newfile.trr -s struct.gro -pbc mol -ur compact
> 
> but I'm not able to obtain that which desire. If I put the protein at the
> center of box, the water begin to translate and rotate. This effect is
> same as deja vu, only that case change the actor (after protein, next
> water). What can I do? Thanks for the help.

What is it that you want?  Your first message said this was a problem using VMD, 
that your system could not be visualized correctly.  Seems to me that if the 
protein's movement is the problem, then any of the above should be adequate.

If you are trying to correct for periodicity for all species in the system 
(protein and water) then a few iterations of trjconv may be necessary, i.e. 
-center (on protein), followed by -pbc nojump or -pbc mol -ur compact.  Using 
trjconv is a bit hit-or-miss, and just requires a bit of playing to get things 
working how you want them.

If you actually want to measure distances (from your previous mail), then leave 
the trajectory alone and use g_dist.

-Justin

>>
>> Alessandro.Maiorana at roma2.infn.it wrote:
>>> Mol is not a pbc's option. I want to remove PBC because, during the
>>> simulation, the protein to get close to the border of the box. This
>>> effect
>>> generate any consequence when I observe the trajectories using the
>>> software VMD. Moreover the distances protein-water are wrong. Thanks for
>>> the helps.
>> There are several options.
>>
>> 1. Upgrade your Gromacs version; I believe -pbc mol came around version
>> 3.3.3,
>> so you must be using an outdated version of the software.
>>
>> 2. Try other trjconv options, like -center or -fit rot+trans to keep your
>> protein centered visually.
>>
>> -Justin
>>
>>>> Alessandro.Maiorana at roma2.infn.it wrote:
>>>>> Hi all,
>>>>>
>>>>> what can I remove the PBC using trjconv? I used the following command:
>>>>>
>>>>> trjconv_d -f traj.trr -s topol.tpr -pbc nojump
>>>> I've had pretty good success using:
>>>>
>>>> trjconv -pbc mol -ur compact
>>>>
>>>> -Justin
>>>>
>>>>> Thanks
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>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Graduate Research Assistant
>>>> 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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>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> 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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> 
> 

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

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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