[gmx-users] H2 topology

[Mark Abraham]

On 02/02/10 14:23, 011013021-Jyotsna wrote:
>
> Dear David,
> Thank you very much for your help.
> As per the literature am following , it is mentioned that the bond
> distance used is 0.7 Angstrom. Where do I incorporate the bond distance
> parameter in the topology file?

See example in chapter 5 of the manual.

> The problem am facing is that , I am not
> very clear as to if the distance is between the two Hydrogen atoms of
> btween the dummy atom and each of the Hydrogen atoms in either side, in
> which case the total distance becomes 1.4 A.

Surely the text of the original article is more clear than that. In any 
case, from where did you get the number 0.7439756 in your topology?

> When i mention the bond distance in the topology file , should it be
> placed under Bond or constraint?

The article surely specifies the nature of the bonded interaction. Work 
out what that is, and then consider the tables in section 5.7.1.

Science in general and computational science in particular is very 
exacting. For your own sake, please cultivate that habit :-)

Mark

> Thank you,
> Jyotsna
>
>
> Re: [gmx-users] H2 topology
> David van der Spoel
> Mon, 01 Feb 2010 04:02:06 -0800
>
> 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
>
>