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

[Golshan Hejazi]

Thanks Bjorn,
These are all good info and for sure helpful. However, I am thinking there should be some easier way in GROMACS because there is "typeB    chargeB   " feature in gromacs top file which seems to be related to the B-state when doing thermodynamics integration. 
But I could not find any documentation how to modify it for charmm force field. this page for example is showing how to do it for a gromacs force field: 

http://compbio.biosci.uq.edu.au/education/Free-Energy_Course/2.hydration-fe.html


I dont know how to modify the "bond, angle and dihedral" section!

Thanks
G.



On Wednesday, January 15, 2014 2:16 PM, Björn Sommer <bjoern at CELLmicrocosmos.org> wrote:
 
> 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
> Message-ID:
>     <1389797062.81229.YahooMailNeo at web140605.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> 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

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