[gmx-users] trjconv_d

[Justin A. Lemkul]

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so you must be using an outdated version of the software.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

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