[gmx-users] Re: Generating Pairs with a Buckingham Potential

[Mark Abraham]

On 30/12/2011 5:30 AM, Olivia Waring wrote:
> Hi Mark,
>
> Thanks for your reply! I'm sorry, you're right, as far as I know the 
> manual doesn't actually mention Buckingham pairs generation... but 
> when I set gen-pairs to "yes" and run grompp, I get the following error:
>
> "Generating pair parameters is only supported with LJ non-bonded 
> interactions"
>
> I guess I'm wondering how anyone can use the Buckingham potential at 
> all, since Gromacs does not appear to support pairs generation for the 
> Buckingham or the use of explicitly defined Buckingham pair parameters 
> (when defining [ pairtypes ], you have to give the parameters in LJ 
> form).

Why do you need pairs with your model?

Mark

>
> Thanks so much again,
> Olivia
>
>
> On Wed, Dec 28, 2011 at 8:28 PM, Mark Abraham <mark.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>> wrote:
>
>     On 29/12/11, *Olivia Waring *<owaring at princeton.edu
>     <mailto:owaring at princeton.edu>> wrote:
>>     I apologize for the truncated message; I pressed send too soon.
>>
>>     According to the Gromacs manual, pairs cannot be generated
>>     automatically for the Buckingham potential,
>     Where does it say this?
>>     but the [ pairtypes ] directive seems to only accept parameters
>>     in LJ form (i.e. c6 and c12, instead of a, b, and c6). I've been
>>     looking into ways to interconvert between the two potential
>>     forms, but haven't found anything... Can anyone who has
>>     successfully generated a topology using the Buckingham potential
>>     shed light on this issue?
>     You want a 1-4 interaction using Buckingham functional form? If
>     so, I don't think GROMACS supports it. If you're trying to combine
>     bits of force fields that use L-J with bits of force fields that
>     use Buckingham, then that's almost certainly a bad idea.
>     Mark
>>
>>     Thank you so much,
>>     Olivia
>>
>>     On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring
>>     <owaring at princeton.edu <mailto:owaring at princeton.edu>> wrote:
>>
>>         Hello Gromacs users,
>>
>>         I'm using a Buckingham potential for the nonbonded
>>         interactions in my system, so I have the following lines in
>>         my forcefield.itp file:
>>
>>         [ defaults ]
>>         ; nbfunc        comb-rule       gen-pairs       fudgeLJ      
>>           fudgeQQ
>>           2             1               no              1.0          
>>           1.0
>>
>>
>>
>>
>>         -- 
>>         Olivia Waring (???)
>>         Princeton University '12
>>         AB Chemistry
>>
>>
>>
>>
>>     -- 
>>     Olivia Waring (???)
>>     Princeton University '12
>>     AB Chemistry
>>
>
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