[gmx-users] SDS initial setup

[zaved at tezu.ernet.in]

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.

Kindly guide me.

Thank You

Regards
Zaved H.


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