[gmx-users] Lennard-Jones 9-6 potential problems

[Berk Hess]

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
> To: 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	spoel at gromacs.org   http://folding.bmc.uu.se
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