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

[Olivia Waring]

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).

Thanks so much again,
Olivia


On Wed, Dec 28, 2011 at 8:28 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> On 29/12/11, *Olivia Waring *<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>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 (王维娅)
>> Princeton University '12
>> AB Chemistry
>>
>>
>
>
> --
> Olivia Waring (王维娅)
> Princeton University '12
> AB Chemistry
>
>
>
> --
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