[gmx-users] SDS initial setup

Justin Lemkul jalemkul at vt.edu
Thu Jan 18 13:40:08 CET 2018

On 1/18/18 7:28 AM, zaved at tezu.ernet.in wrote:
> Dear Gromacs Users
> I am trying to simulate a protein with 200 SDS molecules.
> After inserting 200 molecules inside the box with the protein at the
> center (size of the cubic box is 324 nm3), few of the SDS molecules are
> outside the box from each side of the box.
> I have used the following command to insert the sds molecules:
> gmx insert-molecules -f prot.gro -ci sds.pdb -nmol 200 -o comp.gro
> Will it be appropriate to run simulation with this initial setup? Or do I
> need to make sure that entire sds molecules are inside the box.

There is no such thing as "outside" a periodic box.



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


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