[gmx-users] H2 topology

011013021-Jyotsna 011013021 at bioinfo.sastra.edu
Tue Feb 2 04:23:08 CET 2010

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

Thank you,

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 
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 
.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 
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 
Also the constant probably has to be 0.5 since you want 
the vsite in the center of the two atoms.

Thank you,


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