[gmx-users] -d for all boxtypes

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jul 27 17:56:43 CEST 2015

Hi Sana,

Yes, it's pretty much one value to put them all and in the PBC system
separate them. Except for the rectangular box, the box is set up based on
the circumscribed radius of the solute dilated with the distance d. For the
rectangular box it's based on the extent of the protein in x/y/z.



On Sun, Jul 26, 2015 at 7:14 PM, Sana Saeed <bioinformatic.lady at yahoo.com>

> hi , i am having problems in finding the -d for all box types, like i
> always use cubic box  with -d 1.0, can any one help me in choosing -d for
> other box types, like triclinic , dodecahedron etc. will it be one value
> for all??
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Tsjerk A. Wassenaar, Ph.D.

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