[gmx-users] SDS initial setup

[Dallas Warren]

A visualisation to help see what is going on with the PBC and the
molecules https://twitter.com/dr_dbw/status/909559339366572032
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 19 January 2018 at 01:03, André Farias de Moura <moura at ufscar.br> wrote:
> 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
>>
>> --
>> ==================================================
>>
>> 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
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>>
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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
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