Dear Mark,
Thank you very much for your suggestions.
In the enzyme I am trying to simulate , I need to add 100
H2 molecules (H2+dummy).
when I tried adding H2 through genion , i came to know
genion supports only monoatomic molecules.
My aim is to replace 100 water molecules randomly by H2.
How should I go about it?
With warm regards
Jyotsna
,
On Tue, 02 Feb 2010 16:51:19 +1100
Mark Abraham <[email protected]> wrote:
*This message was transferred with a trial version of
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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
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