[gmx-users] Introducing DUMMY atom and top file modification
bjoern at CELLmicrocosmos.org
Wed Jan 15 20:13:15 CET 2014
> 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
> <1389797062.81229.YahooMailNeo at web140605.mail.bf1.yahoo.com>
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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:
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
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:
It is a similar problem, maybe it provides you some hints.
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