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
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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