On 8/9/12 7:02 PM, Paula Andrea Delgado Pinzon wrote:
Good afternoon, I run a molecular dynamics simulation of two protein complex
with periodic boundaries, when i check the trajectory file i realized that
the molecules were split so i decided to use the trjconv command with the
option -pbc, i tried with -pbc atom, -pbc res and they didn't seem to work or
i am not very sure what they do, but whet i used -pbc whole i achieved
complete molecules but they are supposed to be in contact but it seem that
this option (whole), besides fixing the problem of split molecules they put
the in different positions (before i run trjconv the complex was bind, after
the proteins are unbound). Another question is that after MD simulation i
calculate distances between the two proteins along through with the command
g_dist, i want to know if this calculation is correct even if don't fix the
trajectory
g_dist can handle periodicity internally.
Correctly accounting for periodicity effects often requires several invocations
of trjconv. Consult the following:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
For most systems, trjconv -pbc mol -ur compact followed by trjconv -center
(often with a custom index group) often does quite nicely.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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