[gmx-users] SDS initial setup

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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