<DIV>>zhangjianguo2002 wrote:<BR>>> <BR>>> <BR>>> Firstly, thanks Berk and David van der Spoel for your replies. Maybe <BR>>> I have not explain my problems clearly, there is only one type of <BR>>> particle,namely one full-atom benzene molecule is replaced by one <BR>>> coarse-grained benzene particle,so there in no non-bonded interactions <BR>>> between different types and comb-rule may not work.<BR>>> in the [ defaults ] section of the ITP file, the defaults power for the <BR>>> repulsion term is 12, if I change it to 9, is that enough if I want to <BR>>> use LJ-9-6 potential? is there still anything needed to be changed?<BR>>> <BR>>That is not enough. Please read carefully our previous answers.</DIV>
<DIV> </DIV>
<DIV>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 ?</DIV>
<DIV> </DIV>
<DIV><BR>><BR>>> Best regards!<BR>>> <BR>>> <BR>>> >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>>> ></DIV>
<DIV> </DIV>
<DIV>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?</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR>>> >Berk<BR>>> ><BR>>> >> Date: Tue, 26 May 2009 09:45:22 +0200<BR>>> >> From: spoel@xray.bmc.uu.se <mailto:spoel@xray.bmc.uu.se><BR>>> >> To: gmx-users@gromacs.org <mailto: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>>> >> </DIV>
<DIV> </DIV>
<DIV>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?<BR></DIV>
<DIV> </DIV>
<DIV>>> >> <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>>> >> > ´©Ã½µÃÃð´ø ¼ÃÃîãë´¨µÃÃðûÃÃÃê <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 <mailto: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 <mailto: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 <mailto:spoel@xray.bmc.uu.se>        spoel@gromacs.org <mailto:spoel@gromacs.org> http://folding.bmc.uu.se<BR>>> >> _______________________________________________<BR>>> >> gmx-users mailing list gmx-users@gromacs.org <mailto: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 <mailto:gmx-users-request@gromacs.org>.<BR>>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>>> ><BR>>> >_________________________________________________________________<BR>>> >See all the ways you can stay connected to friends and family<BR>>> >http://www.microsoft.com/windows/windowslive/default.aspx<BR>>> >-------------- next part --------------<BR>>> >An HTML attachment was scrubbed...<BR>>> >URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090526/2143fc5e/attachment.html<BR>>> ><BR>>> >------------------------------<BR>>> ><BR>>> >_______________________________________________<BR>>> >gmx-users mailing list<BR>>> >gmx-users@gromacs.org <mailto: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>>> ><BR>>> >End of gmx-users Digest, Vol 61, Issue 124<BR>>> >******************************************<BR>>> <BR>>> <BR>>> <BR>>> ------------------------------------------------------------------------<BR>>> ç©¿è¶å°é带 纪念汶å·å°éä¸å¨å¹´<BR>>> <http://512.mail.163.com/mailstamp/stamp/dz/activity.do?from=footer> <BR>>> <BR>>> <BR>>> <BR>>> ------------------------------------------------------------------------<BR>>> ç©¿è¶å°é带 纪念汶å·å°éä¸å¨å¹´ <BR>>> <http://512.mail.163.com/mailstamp/stamp/dz/activity.do?from=footer><BR>>> <BR>>> ------------------------------------------------------------------------<BR>>> ç©¿è¶å°é带 纪念汶å·å°éä¸å¨å¹´ <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>><BR>>------------------------------<BR>><BR>>_______________________________________________<BR>>gmx-users mailing list<BR>>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>><BR>>End of gmx-users Digest, Vol 61, Issue 129<BR>>******************************************<BR></DIV><br><!-- footer --><br><span title="neteasefooter"/><hr/>
<a href="http://512.mail.163.com/mailstamp/stamp/dz/activity.do?from=footer">穿越地震带 纪念汶川地震一周年</a>
</span>