[gmx-users] H2 topology

[David van der Spoel]

On 2/1/10 10:57 AM, 011013021-Jyotsna wrote:
> Dear all,
>
> I want to run a simulation for an enzyme. It demands me to incorporate a
> Molecular hydrogen Topology with a dummy atom in between in the
> simulation in order to study the path of hydrogen in it.The problem is ,
> the topology file I built induces many errors when i come to the energy
> minimization step. The version of gromacs I am using is 4.0. The
> topology file I built is as follows
>
>
>
> [ moleculetype ]
> ;name nrexcl
> H2 3
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass ; total charge
> 1 H 1 H2 H1 1 0.475 1.00800 ; 0.00
> 2 H 1 H2 H2 1 0.475 1.00800 ; 0.00
> 3 DUM 1 H2 DUM 1 -0.950 0.000
>
> [ virtual_sites2 ]
> ; Site from funct a
> 3 1 2 1 0.7439756
>
>
> When ever I insert the hydrogen+dummy atom topology in the protein's
> .gro file, an error is generated regarding mismatch of residues or the
> dummy atom having mass 0 .
>
> I would be really grateful if anyone could provide me the hydrogen
> molecule topology and give some pointers towards it.
>

Please print the error message in your mail.

Topology look OK, but you need to add a bond or constraint.
Also the constant probably has to be 0.5 since you want the vsite in the 
center of the two atoms.


> Thank you,
>
> Jyotsna
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se