[gmx-users] multiple molecules of same type and .top file

[Justin Lemkul]

On 5/12/14, 2:43 AM, Chetan Mahajan wrote:
> Dear All,
>
> I am trying to generate .top file for my system. I would be obliged if you
> could explain following topology file question to me, since it is not very
> clearly mentioned anywhere:
>
> In LAMMPS software that I am used to, user is required to enter details of
> topology for all the molecules of same type e.g. if there are 1000 formate
> ions, one needs to enter atoms, bonds, angles, dihedrals for all 1000
> formate ions. Is this the case for GROMACS or only one representational
> topology for 1 molecule of that type is sufficient? Atoms section in .top
> file in gromacs does contain column for residue number (resi or resnr) in a
> given [moleculetype], so I would guess probably I need to enter all the
> molecules of a given type, although it is not the case for water?
>

The purpose of the [molecules] directive in the topology is so you don't have to 
explicitly repeat information.  If you have X molecules of some species defined 
in a [moleculetype], you just enter X as the number of molecules in [molecules]. 
  That's the way water is handled.  The #include statement for the water 
topology says, "here's the definition of what SOL is," and then [molecules] 
says, "repeat that information for the next X molecules in the configuration."

The resnr column in the [atoms] directive is most commonly used for polymers, 
i.e. proteins, DNA, etc.  You could define multiple topologically identical 
molecules as a multi-molecule [moleculetype], but it's not required.

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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