[gmx-users] Basic questions

[Justin Lemkul]

On 12/30/16 12:46 PM, qasimpars at gmail.com wrote:
> Dear users,
>
> I have some questions on MD simulations:
>
> 1.) I usually come accross in my GROMACS simulations: the atoms of the system jump accross the box. Why do the atoms of the system jump accross the box?
>

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

> 2.) In GROMACS the minimum image convention is like in this link, right?
> http://www.compsoc.man.ac.uk/~lucky/Democritus/Theory/pbc-mi.html
>

Yes, the same as any MD software.

> That means that the real simulation cell surrounds with 8 boxes/cells as in the above link??
>

There are 26 images around the central unit cell.  The simulation is in 3D, not 
just 2D like that image.

> 3.) Before starting simulation, I enumerate the ligand residue as a 1 (1LIG) in the starting file. After energy minimization, GROMACS renumber the ligand residue in the output gro file, e.g. 150 (150LIG). However the residue number of ligand in the ligand.itp is 1. In spite of that GROMACS doesn't give any error with the renumbered ligand 150LIG in the input file (complex.gro) for the next steps (nvt, npt and production). How GROMACS doesn't get confused with the different residue number of ligand in the ligand.itp (1LIG) and complex.gro file (150LIG)?
>

Topological numbering and coordinate numbering do not need to match.  The 
topology *must* be numbered from 1 in each [moleculetype] based on how the 
topological information is parsed.  But that species can then have any global 
coordinate numbering.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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