[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

[Darrell Koskinen]

Hi Mark,
I thought opls_127 and opls_128 were the representative atoms to use for 
ammonia. Please correct me if I am wrong.

Would the adsorption of the polar ammonia molecule onto the polar 
(hydrogen-terminated) edges of the graphene sheet be affected by the 
missing LJ parameter on the H atoms?

Thanks.

Darrell
> Date: Mon, 26 Oct 2009 08:47:14 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
> 	ffoplsaa
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4AE4C762.2060609 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Justin A. Lemkul wrote:
>   
>> Darrell Koskinen wrote:
>>     
>>> I looked through the ffoplsaanb.itp file and see that all the H atoms 
>>> except for the following four have zero LJ parameters:
>>>
>>> HC OPLS_140 alkane H
>>> HA OPLS_146 Benzene H
>>> H4 OPLS_345 Cytosine H-C6
>>> H5 OPLS_355 Adenine & Guanine H-C2
>>>
>>> However, in the paper "Development and Testing of the OPLS All-Atom 
>>> Force Field on Conformational Energetics and Properties of Organic 
>>> Liquids", it states: "The original OPLS (optimized potentials for 
>>> liquid simulations) potential functions used a partially united-atom 
>>> (UA) model; sites for nonbonded interactions are placed on all 
>>> nonhydrogen atoms and on hydrogens attached to heteroatoms or carbons 
>>> in aromatic rings". Later, the paper indicates that the paramters were 
>>> adopted as much as possible from the OPLS-UA force field. Thus, since 
>>> "sites for nonbonded interactions are placed on hydrogens attached to 
>>> heteroatoms ", it appears to me that a site for a non-bonded 
>>> interaction should exist on the H atoms within ammonia. Is my 
>>> interpretation incorrect?
>>>
>>>       
>> I don't think so.  Each of the above examples you've cited above is for 
>> a C-H bond in an aromatic ring.  In OPLS, all N-H bonds involved 
>> hydrogen atoms with zero LJ parameters.  See, for example, any backbone 
>> NH, amide (ASN/GLN), or amine (LYS/LYSH), etc and you will see the atom 
>> types used.
>>     
>
> I think you're both partly wrong. Type 140 is not for C-H in an aromatic 
> ring, and if you grep 1.008 ffoplsaanb.itp you get many more H atom 
> types with LJ. Certainly Justin's right inasmuch as amide N-H type 241 
> has no H LJ parameters. Perhaps there's other text that Darrell hasn't 
> found yet, or backbone nitrogen is not considered a heteroatom :-).
>
> Mark
>
>   
>>> Darrell
>>>       
>>>> Date: Mon, 19 Oct 2009 19:07:22 +1100
>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>>> Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
>>>>     ffoplsaa
>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>> Message-ID: <4ADC1E3A.8010502 at anu.edu.au>
>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>
>>>> Darrell Koskinen wrote:
>>>>  
>>>>         
>>>>> Hi,
>>>>> I see that the Lennard Jones parameters for the N & H atoms in 
>>>>> ammonia, represented by opls_127 and opls_128 in the file 
>>>>> ffoplsaanb.itp are:
>>>>>
>>>>> opls_127   NT  7     14.00670    -1.020       A    3.42000e-01  
>>>>> 7.11280e-01
>>>>> opls_128   H   1       1.00800     0.340       A    0.00000e+00  
>>>>> 0.00000e+00
>>>>>
>>>>> Why are sigma and epsilon both zero for H? Are the LJ parameters for 
>>>>> H embedded in the parameter for NT? If so, how were these parameters 
>>>>> combined?
>>>>>     
>>>>>           
>>>> What do other H have? What do the OPLS-AA paper(s) have to say about 
>>>> such H atoms?
>>>>
>>>> Mark
>>>>