011013021-Jyotsna wrote:
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?
genconf -ci
-Justin
With warm regards
Jyotsna
,
On Tue, 02 Feb 2010 16:51:19 +1100
Mark Abraham <mark.abra...@anu.edu.au> wrote:
*This message was transferred with a trial version of CommuniGate(r) Pro*
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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