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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 23 09:42:45 CEST 2012


> 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.

Well, it's not the most compact (otherwise -ur compact would yield you
a brick again), but it's the easiest, and the easiest to build with a
rectangular bricklet of solvent. Mind that this is explained in quite
some detail in the manual, in numerous posts in the user list
archives, and in tutorial material. Oh, and also do note that there is
no need to do any conversion with trjconv, unless you aim at pretty



> -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.
>>    --
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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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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