[gmx-users] Pbc

[Justin Lemkul]

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... 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

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

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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