[gmx-users] How to implement LJ 6-12 function form?

[David van der Spoel]

On 2014-10-29 03:26, Kester Wong wrote:
>
> I was puzzled by that before, as the LJ interactions by the
> Lorenzt-Berthelot comb-rules (page 68) looked exactly like the LJ 6-12
> function form.
>
> Hence I was thinking how can one use the comb-rule type2 (carbon-water
> nonbond-param) and LJ 6-12 (table6-12.xvg) together.
you can specify a whole matrix of nonbonded parameters if you wish.
>
> Thank you Eric!
>
>
>
> Cheers,
>
> Kester
>
> --------- 원본 메일 ---------
>
>     *보낸사람* : Eric Smoll <ericsmoll at gmail.com>
>     *받는사람* : <gmx-users at gromacs.org>
>     *받은날짜* : 2014년 10월 29일(수) 10:51:54
>     *제목* : Re: [gmx-users] How to implement LJ 6-12 function form?
>
>     Hello Kester,
>
>     Setting the first value in the defaults directive to 1 indicates that you
>     want to use the 6-12 LJ potential. As far as I understand, setting N is
>     only necessary if you want the repulsive LJ term to be something other than
>     12. I don't think you need to do anything else. The first defaults entry
>     looks good.
>
>     See page 144 of the Gromacs 5.0.2 manual.
>
>     Best,
>     Eric
>
>     On Tue, Oct 28, 2014 at 7:40 PM, Kester Wong  wrote:
>
>     > Dear all,
>     >
>     >
>     > I am using GROMACS 5.0, could anyone tell me how can I use the LJ 6-12 in
>     > my calculations?
>     >
>     > My force field [ defaults ] is as follows:
>     >
>     >
>     > [ defaults ]
>     >
>     > ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>     >
>     > 1               2               yes             0.5     0.5
>     >
>     >
>     > According to the manual, do I add "N" equals to 12 to enable the LJ 6-12
>     > (carbon-water) interaction parameters to be used, without using the look up
>     > table "table6-12.xvg"?
>     >
>     >
>     > [ defaults ]
>     >
>     > ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ    N
>     >
>     > LJ               2               yes             0.5     0.5
>     >           12
>     >
>     > My current system already has the following parameters bonding,
>     > nonbonding, graphene, water and ions topologies; based on the TIPS3P and
>     > CHARMM27 models.
>     >
>     > Thanks for any input!
>     >
>     > Regards,
>     > Kester
>     >
>     >
>     >
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se