[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
> your_aim.pdb

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 
expected visualization.


> 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?
>     Thanks.
>     --
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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