[gmx-users] H2 topology
011013021 at bioinfo.sastra.edu
Tue Feb 2 11:37:11 CET 2010
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
On Tue, 02 Feb 2010 16:51:19 +1100
Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> *This message was transferred with a trial version of
> 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 :-)
>> 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
>> 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
>> 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
>> .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
>> 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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