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Hi,<br><br>I forgot about this feature.<br>Your problem is indeed that you used comb-rule=1,<br>you have to use 2 or 3 to make this work.<br>And indeed you should use user tables filled with the 9-6 potential.<br><br>Gromacs could actually easily support p-6 tables with any value for p,<br>by storing p in the tpr file and automatically using tables when p!=12.<br><br>Berk<br><br>> Date: Tue, 26 May 2009 09:45:22 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Lennard-Jones 9-6 potential problems<br>> <br>> zhangjianguo2002 wrote:<br>> > Hi everyone!<br>> > Have anyone used the Lennard-Jones 9-6 potential for coarse-grained <br>> > models? when I use it, I get a very different result from that is got <br>> > from the same Lennard-Jones 9-6 potential formed a potential table,the <br>> > latter's results are comparable to the experiments. when I use LJ-9-6 <br>> > potential,the ITP file is as following:<br>> > <br>> > [ defaults ]<br>> > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>> > 1 1 no 1.0 1.0 9<br>> <br>> Even if this may generate the correct parameters (please use gmxdump to <br>> check your tpr file) you still have to provide a user table to mdrun and <br>> to set vdw-type = user in your mdp file. You may need to change the <br>> nbfunc to three as well. Check source code in src/kernel/convparm to see <br>> what is going on. I don't think this is documented anywhere, is it?<br>> <br>> <br>> > <br>> > [ atomtypes ]<br>> > ; name bond_type mass charge ptype sigma epsilon<br>> > opls_001 Cx 6 78.0190 0 A 0.505 2.95;<br>> > <br>> > [ moleculetype ]<br>> > ; Name nrexcl<br>> > Phenyl 1<br>> > [ atoms ]<br>> > ; nr type resnr resid atom cgnr charge mass<br>> > 1 opls_001 1 Phenyl C1 1 0.000 78.0190 <br>> > <br>> > other files ,such as mdp file and top file ,are all the same as normal <br>> > LJ-12-6 potential, are these correct if I want to use LJ-9-6 potential? <br>> > Do I still need to change something? Thanks very much for your kindness!<br>> > <br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > 穿越地震带 纪念汶川地震一周年 <br>> > <http://512.mail.163.com/mailstamp/stamp/dz/activity.do?from=footer><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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