[gmx-users] related to box dimension : solvate protein-ligand complex

[Justin Lemkul]

On 6/4/18 4:19 AM, Quyen V. Vu wrote:
> Hi,
> As i know that vmd cannot understand dodecahedron, he will take 3 numbers
> and plot a cubic while your box still is dodecahedron
>

VMD will display whatever coordinates it is given. GROMACS will, by 
default, write coordinates using a triclinic representation of the unit 
cell. One can "unwrap" the coordinates with trjconv, and in that case, 
VMD will display exactly the unit cell shape that is defined, and it 
certainly understands dodecahedral and octahedral shapes.

-Justin

> On Fri, Jun 1, 2018, 06:48 Seketoulie Keretsu <sekekeretsu at gmail.com> wrote:
>
>> Dear All,
>>
>> I am doing he Protein-ligand complex tutorial on gromacs 5.0.7 (newly
>> installed). I have successfully completed this tutorial earlier on
>> gromacs 4.6.
>>
>> After the solvation step I found out that the protein-ligand complex
>> solvated system had a cubic shape while my box dimension (shown using
>> vmd command: pbc box) adopted a dodecahedron like shape. Please check
>> the attachment for details.
>>
>> What could be the possible reason behind this? Kindly advise to
>> rectify the problem.
>>
>> The was no error or warning uptill this.
>>
>> Thank you.
>>
>> Sincerely,
>>
>> Seke
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-- 
==================================================

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.thelemkullab.com

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