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

[David van der Spoel]

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