[gmx-users] Minimization changes system box shape after using ParmEd

Justin Lemkul jalemkul at vt.edu
Fri Jan 5 00:04:12 CET 2018

On 1/4/18 5:42 PM, Crystal Vander Zanden wrote:
> Hello GROMACS community,
> I am having problems maintaining the shape of my system box after using
> ParmEd to convert from Amber to Gromacs format.
> I parameterized a system with AmberTools (peptide solvated in an octahedral
> box).  I then converted the Amber files (.inpcrd and .prmtop) to GROMACS
> format (.gro and .top) using ParmEd.  I used VMD to look at the system, and
> it looks ok (peptide still centered in an octahedral box). (
> http://i1380.photobucket.com/albums/ah185/cmvander/parmed_zpssaq6ldnb.png)
> Next I did an energy minimization in GROMACS.  VMD displayed the resulting
> .gro file as a triclinic box and the peptide is no longer centered. (
> http://i1380.photobucket.com/albums/ah185/cmvander/minimized_zpsekznpl3w.png
> )
> I think that the system really is still an octahedral box because I can see
> the octahedral box boundaries within the triclinic box. I overlaid both
> systems and the protein is in the same spot (
> http://i1380.photobucket.com/albums/ah185/cmvander/image_overlay_zpsepfpqkvl.png).
> Also I got reasonable minimization energies.
> Steepest Descents converged to Fmax < 1000 in 337 steps
> Potential Energy  = -3.1393012e+05
> Maximum force     =  9.0675385e+02 on atom 363
> Norm of force     =  3.5674736e+01
> Am I just doing something wrong to cause VMD to display my system
> incorrectly, or is there a more serious issue?  Either way, I’d be happy to
> know how to fix it!

GROMACS always uses a triclinic representation by default. Convert it to 
the desired shape with trjconv:

gmx trjconv -pbc mol -ur compact



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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