[gmx-users] Lyzosyme with ligand tutorial

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 24 22:14:48 CEST 2011

James Starlight wrote:
> Justin,
> I've used trjconv -pbc mol -ur compact 
> but the final picture was still wrong :(
> So I think that something happened with my box  because
> 1- If the cubic representation is set on default why other .gro 
> structures were visualized in VMD in dodecahedral box on default ?

VMD always defaults to a triclinic representation (since that is what is stored 
in Gromacs by default) unless the PBC is wrapped with -pbc mol -ur compact.  If 
VMD truly produces the pseudospherical shape, then trjconv was invoked somewhere 
along the way.

> 2- Why the pereodic boundaries were distorded in the next stage after 
> NPT   (production MD) that my structure were outside the box on half ? I 
> want to point that on MD stage the box were dodecahedral again like in 
> the NVT and other stages but my structure was in wrong position.

I don't understand this statement.  You should also note that a periodic box has 
no "outside."  Perhaps it would be useful to post images online.  If you choose 
to do so, please follow bullet point #4 here:




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


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