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

[Crystal Vander Zanden]

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
em.tpr

Thank you for your help!
Crystal



> 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!
>
> Thanks in advance for any advice!  I really appreciate it!
> Crystal
>
>
> ------------------------------
>
> GROMACS always uses a triclinic representation by default. Convert it to
> the desired shape with trjconv:
>
> gmx trjconv -pbc mol -ur compact
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>