[gmx-users] H2 topology

[Thomas Piggot]

I think Justin meant genbox -ci

Tom

Justin A. Lemkul wrote:
> 
> 
> 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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>>
> 

-- 
Thomas Piggot
University of Bristol, UK.