[gmx-users] Lennard-Jones 9-6 potential problems
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 27 09:40:46 CEST 2009
zhangjianguo2002 wrote:
> >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.
>
> Thanks very much for your suggestions! I just want to use LJ-9-6
> potential by providing sigma and epsilon parameters, that would be easer
> to change the potential by changing sigma and epsilon values than by
> changing potential table, does GROMACS support this ? or does GROMACS
> only support potential tables if the power of the repulsion term is not 12 ?
>
It is the other way around. GROAMCS only support native code for 12-6
and Exp-6, for everything else you need tables. But grompp can compute
the C9,C6 params from eps/sig. Use gmxdump to check your input.
>
> >
> >> 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.
> >> >
>
> Thanks for your reply, do you mean that if p !=12 ,I have to change p to
> the value I want ,at the same time I have to provide a potential table
> according to LJ-P-6?
>
>
>
> >> >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?
> >> >>
>
> Thanks very much for your advice! According to you , I provide a user
> table( Does this mean that LJ'parameters epsilon and sigma setted in the
> ITP file don't work ? ) and set vdw-type = user as well as change nbfunc
> to three ,but grompp reports some errors that : "Invalid nonbond
> function selector '3' using LJ",I read the manual again,it says :
> non-bond type =1(Lennaed-Jones) or 2(Buckingham), that is seemed that 3
> is a illegal choice, is there something wrong?
>
> >> >>
> >> >> >
> >> >> > [ 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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--
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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