[gmx-users] Lennard-Jones 9-6 potential problems
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 27 08:19:55 CEST 2009
zhangjianguo2002 wrote:
>
>
> Firstly, thanks Berk and David van der Spoel for your replies. Maybe
> I have not explain my problems clearly, there is only one type of
> particle,namely one full-atom benzene molecule is replaced by one
> coarse-grained benzene particle,so there in no non-bonded interactions
> between different types and comb-rule may not work.
> in the [ defaults ] section of the ITP file, the defaults power for the
> repulsion term is 12, if I change it to 9, is that enough if I want to
> use LJ-9-6 potential? is there still anything needed to be changed?
>
That is not enough. Please read carefully our previous answers.
> Best regards!
>
>
> >Hi,
> >
> >I forgot about this feature.
> >Your problem is indeed that you used comb-rule=1,
> >you have to use 2 or 3 to make this work.
> >And indeed you should use user tables filled with the 9-6 potential.
> >
> >Gromacs could actually easily support p-6 tables with any value for p,
> >by storing p in the tpr file and automatically using tables when p!=12.
> >
> >Berk
> >
> >> Date: Tue, 26 May 2009 09:45:22 +0200
> >> From: spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> >> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> >> Subject: Re: [gmx-users] Lennard-Jones 9-6 potential problems
> >>
> >> zhangjianguo2002 wrote:
> >> > Hi everyone!
> >> > Have anyone used the Lennard-Jones 9-6 potential for coarse-grained
> >> > models? when I use it, I get a very different result from that is got
> >> > from the same Lennard-Jones 9-6 potential formed a potential table,the
> >> > latter's results are comparable to the experiments. when I use LJ-9-6
> >> > potential,the ITP file is as following:
> >> >
> >> > [ defaults ]
> >> > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> >> > 1 1 no 1.0 1.0 9
> >>
> >> Even if this may generate the correct parameters (please use gmxdump to
> >> check your tpr file) you still have to provide a user table to mdrun and
> >> to set vdw-type = user in your mdp file. You may need to change the
> >> nbfunc to three as well. Check source code in src/kernel/convparm to see
> >> what is going on. I don't think this is documented anywhere, is it?
> >>
> >>
> >> >
> >> > [ atomtypes ]
> >> > ; name bond_type mass charge ptype sigma epsilon
> >> > opls_001 Cx 6 78.0190 0 A 0.505 2.95;
> >> >
> >> > [ moleculetype ]
> >> > ; Name nrexcl
> >> > Phenyl 1
> >> > [ atoms ]
> >> > ; nr type resnr resid atom cgnr charge mass
> >> > 1 opls_001 1 Phenyl C1 1 0.000 78.0190
> >> >
> >> > other files ,such as mdp file and top file ,are all the same as normal
> >> > LJ-12-6 potential, are these correct if I want to use LJ-9-6 potential?
> >> > Do I still need to change something? Thanks very much for your kindness!
> >> >
> >> >
> >> >
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> >> --
> >> David van der Spoel, Ph.D., Professor of Biology
> >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> >> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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