[gmx-users] H2 topology

[Justin A. Lemkul]

Thomas Piggot wrote:
> I think Justin meant genbox -ci
> 

Indeed, that is correct!  Thanks for pointing that out.  I know I shouldn't 
reply in the morning before I am thoroughly caffeinated...

-Justin

> 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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>>>
>>
> 

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

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

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