[gmx-users] trjconv_d

[Alessandro.Maiorana at roma2.infn.it]

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.
>
>
> 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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