[gmx-users] Pbc

Justin Lemkul jalemkul at vt.edu
Thu Aug 17 14:10:39 CEST 2017

On 8/16/17 4:24 PM, farial tavakoli wrote:
>   blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Dear gromacs users
> I need to visualize my md_0_1.tpr , so i issued  trjconv -s md_0_1.tpr -f md_0_1.xtc -o xxx.pdb -pbc nojump -dt 10to remove the jumps over the boundaries and make a continuous trajectoryPBCBut when i visualized my complex by pymol, the protein appeared broken . Would you please help me to solve it?

The molecules are broken because you didn't tell trjconv to make them 
whole.  Google is your friend... 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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