[gmx-users] Introducing DUMMY atom and top file modification

[Björn Sommer]

> Date: Wed, 15 Jan 2014 06:44:22 -0800 (PST)
> From: Golshan Hejazi <golshan.hejazi at yahoo.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] Introducing DUMMY atom and top file modification
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> Hi everyone,
>
> I wanna perform a TI using gromacs. For that I am modifying the top file in order to introduce dummy atoms and I am using charmm ff. I have already introduced a new molecule named PAR and I want to have another molecule in my simulation which is the PAR molecule turned to a DUMMY molecule.
> In the top file, I have these lines for atom section:

Hi Golshan,

I do not know, if this will help. First, I know that the OPM database uses DUMMY atoms to indicate the top and bottom side of membranes. For that, they use a PDB file which contains "DUM" Atom entries, e.g.

HETATM 4986  O   DUM  4986      44.000  10.000  15.700

http://opm.phar.umich.edu

Maybe it would make sense, to keep this notation also for you and maybe you will find somebody who had a similar idea for this kind of protein structures. They are often used for simulations, but I think, usually the DUM atoms are removed prior simulation.

Second, a first search concerning this topic returned this entry:

http://gromacs.5086.x6.nabble.com/dummy-atoms-td4393866.html

It is a similar problem, maybe it provides you some hints.

Best,
Björn