[gmx-users] SDS initial setup

Justin Lemkul jalemkul at vt.edu
Tue Jan 23 16:51:21 CET 2018

On 1/23/18 9:29 AM, zaved at tezu.ernet.in wrote:
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>> Today's Topics:
>>     1. Re: SDS initial setup (Dallas Warren)
>>     2. Is there any difference with gromacs and other MD	programs?
>>        (??? (?????))
>>     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.

What you might be missing is that there is no such thing as "outside" of 
a periodic box. You are looking at the central image of an infinite 
system, so the molecules are always surrounded by images of the 
particles across the boundaries.

> 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?

Convenience. You need to define a size for the central image that 
satisfies the minimum image convention, so we position our solute(s) of 
interest in the center of that image (which again is an arbitrary 
definition when considering an infinite number of representations) and 
compute a box size based on the resulting solute coordinates that will 
provide a suitable buffer to satisfy the MIC.



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

303 Engel Hall
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