[gmx-users] problem with solvent box in gromacs 4.5.4
Justin A. Lemkul
jalemkul at vt.edu
Tue May 22 19:17:05 CEST 2012
On 5/22/12 6:36 PM, mu xiaojia wrote:
> try trjconv, maybe your reference gro/tpr file is cubic?
> make sure:
> trjconv -s the_dodecahedral_generated.tpr -f the_dodecahedral_generated.gro -o
The triclinic representation is used for all boxes in Gromacs as it is the most
compact. One needs to invoke trjconv with "-pbc mol -ur compact" to obtain the
> On Tue, May 22, 2012 at 9:27 AM, patrick wintrode <pat_wde2 at yahoo.com
> <mailto:pat_wde2 at yahoo.com>> wrote:
> After generating my protein .gro and .top files and doing the initial energy
> minimization, I used the following series of commands:
> editconf -f protein-vacuum.gro -o protein-PBC.gro -bt dodecahedron -d 1.2
> genbox -cp protein-PBC.gro -cs spc216.gro -p protein.top -o protein-water.gro
> I then use editconf to convert protein-water.gro to a pdb file. When I open this
> file in PyMol, the water box is cubic rather than dodecahedral.
> Has any one else encountered this?
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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