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so you must be using an outdated version of the software.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