[gmx-users] fixing split molecules in trajectory file

Justin Lemkul jalemkul at vt.edu
Fri Aug 10 01:05:09 CEST 2012

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:


For most systems, trjconv -pbc mol -ur compact followed by trjconv -center 
(often with a custom index group) often does quite nicely.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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