[gmx-users] SDS initial setup
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
>> <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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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