[gmx-users] protein near the edges of simulation box

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 15 18:34:09 CEST 2012

On 6/15/12 12:19 PM, Shima Arasteh wrote:
>   OK, but as I know the trjconv is a command after mdrun, so when I get the
> output of mdrun and see it in VMD, it doesn't make different.
> Now wondering what is the benefit of trjconv -center and -pbc?

You have to load the output trajectory from trjconv into VMD, not the original. 
  If you visualize trajectory A, then manipulate it to produce trajectory B, 
then trajectory B is no use to you unless you actually use it.



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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