[gmx-users] H2 topology

[Justin A. Lemkul]

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.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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> 

-- 
========================================

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

========================================