[gmx-users] SDS initial setup

zaved at tezu.ernet.in zaved at tezu.ernet.in
Tue Jan 23 15:30:02 CET 2018

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>    1. Re: SDS initial setup (Dallas Warren)
>    2. Is there any difference with gromacs and other MD	programs?
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>    3. MDP define in GROMACS 2018 (Joshua Mitchell)
>    4. Cannot find position restraint file restraint.gro (Sailesh Bataju)
> ----------------------------------------------------------------------
> Message: 1
> Date: Mon, 22 Jan 2018 11:42:51 +1100
> From: Dallas Warren <dallas.warren at monash.edu>
> To: GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] SDS initial setup
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> 	<CAOv1qzaVWjsEmxSO+GZf3YZBOF8LZU4=qSRbBO6fhm2jz0dckg at mail.gmail.com>
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Thank you Justin and Dallas for your kind response.

PBC comes into effect from the start of minimization step. As we apply it
in the minim.mdp file as pbc = xyz. However in my case the SDS molecules
appears to be outside during initial setup itself. Kindly correct me if I
missed out something.

However if that is the case, it might sounds vague but I am thinking why
then we center the protein (eg and keep it 1 nm from the edge of the box
to its center) during protein setup?

Thank You


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, Andr? 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

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