[gmx-users] SDS initial setup

[André Farias de Moura]

Besides the fact that there cannot be molecules outside a periodic box, are
you sure that you want such a high SDS concentration? You are nearly 15
times over the cmc, in the real world you would most likely end up with a
hydrated SDS crystals (Mol. Cryst. Liq. Cryst., Vol. 549:pp. 160–165, 2011)

On Thu, Jan 18, 2018 at 10:39 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090