[gmx-users] H2 topology

[011013021-Jyotsna]

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 <Mark.Abraham at 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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