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?
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: sp...@xray.bmc.uu.se
>> To: gmx-us...@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.
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