[gmx-users] problem with solvent box in gromacs 4.5.4

[Justin A. Lemkul]

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.

-Justin

> 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.
>
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================