>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: 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! >> >> > >> >> > >> >> > >> >> > >> ------------------------------------------------------------------------ >> >> > ´©Ã½µÃÃð´ø ¼ÃÃîãë´¨µÃÃðûÃÃÃê >> >> > <http://512.mail.163.com/mailstamp/stamp/dz/activity.do?from=footer> >> >> > >> >> > >> >> > >> ------------------------------------------------------------------------ >> >> > >> >> > _______________________________________________ >> >> > gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> > http://www.gromacs.org/mailman/listinfo/gmx-users >> >> > Please search the archive at http://www.gromacs.org/search before >> posting! >> >> > Please don't post (un)subscribe requests to the list. Use the >> >> > www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> >> -- >> >> 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 >> >> _______________________________________________ >> >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> >> Please search the archive at http://www.gromacs.org/search before >> posting! >> >> Please don't post (un)subscribe requests to the list. Use the >> >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? 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