[gmx-users] Lennard-Jones 9-6 potential problems

[zhangjianguo2002]

   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? 
 
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.
>
>Berk
>
>> Date: Tue, 26 May 2009 09:45:22 +0200
>> From: spoel at xray.bmc.uu.se
>> To: 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?
>> 
>> 
>> > 
>> > [ 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>
>> > 
>> > 
>> > ------------------------------------------------------------------------
>> > 
>> > _______________________________________________
>> > gmx-users mailing list    gmx-users at 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-request at 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.
>> spoel at xray.bmc.uu.sespoel@gromacs.org   http://folding.bmc.uu.se
>> _______________________________________________
>> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>_________________________________________________________________
>See all the ways you can stay connected to friends and family
>http://www.microsoft.com/windows/windowslive/default.aspx
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090526/2143fc5e/attachment.html
>
>------------------------------
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before posting!
>
>End of gmx-users Digest, Vol 61, Issue 124
>******************************************




穿越地震带 纪念汶川地震一周年


穿越地震带 纪念汶川地震一周年
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090527/546835a6/attachment.html>