[gmx-users] Minimization changes system box shape after using ParmEd
Crystal Vander Zanden
cvanderzanden at unm.edu
Fri Jan 5 15:45:16 CET 2018
Thank you Dr. Lemkul,
I used trjconv as you suggested. I also needed to add the -center flag.
gmx trjconv -pbc mol -ur compact -center -f em.gro -o em_trjconv.gro -s
Thank you for your help!
> 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). (
> 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. (
> 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 (
> 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!
> Thanks in advance for any advice! I really appreciate 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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