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: sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
 >>     >> To: gmx-users@gromacs.org <mailto:gmx-users@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! >> >> > >> >> > >> >> > >> >> > ------------------------------------------------------------------------ >> >> > ´©Ô½µØÕð´ø ¼ÍÄîãë´¨µØÕðÒ»ÖÜÄê >> >> > <http://512.mail.163.com/mailstamp/stamp/dz/activity.do?from=footer> >> >> > >> >> > >> >> > ------------------------------------------------------------------------ >> >> > >> >> > _______________________________________________
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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. >> >> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> sp...@gromacs.org <mailto:sp...@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.
 >sp...@xray.bmc.uu.se sp...@gromacs.org   http://folding.bmc.uu.se
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se    sp...@gromacs.org   http://folding.bmc.uu.se
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