[gmx-users] Lennard-Jones 9-6 potential problems
zhangjianguo2002
zhangjianguo2002 at 126.com
Wed May 27 09:33:18 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.
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 ?
>
>> 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
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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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