[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion
james zhang
james.zhangj at gmail.com
Sun Jul 15 16:35:18 CEST 2007
I used rule 3 for ffopls rule 1 for ffgmx.
sigma/epsilon
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
C6/C12
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
Thanks
On 7/15/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> james zhang wrote:
> > I did convert the parameters according to Manual chapter 4.11 and 5.3.3.
> > I used C6=4*epsilon*sigma^6 and C12=4*epsilon*sigma^12 formula.
> > If my conversion is right, then where is wrong?
> how about the defaults section (chapter 5)
> >
> > I find the same question in the mailing list, but there is no response.
> > http://www.gromacs.org/pipermail/gmx-users/2004-July/011337.html
> >
> > Why did the same system get totally different simulation result when I
> > changed the L-J expressions?
> > Thanks.
> >
> > On 7/15/07, *David van der Spoel* <spoel at xray.bmc.uu.se
> > <mailto:spoel at xray.bmc.uu.se>> wrote:
> >
> > james zhang wrote:
> > > Hi,
> > >
> > > I am trying to do some simulation of chloroform system and I need
> > > convert sigma & epsilon to C6 & C12 LJ-parameters.
> > >
> > > I use C6=4*epsilon*sigma^6 and C12=4*epsilon*sigma^12 formula.
> > > This is my result
> > >
> > > [ atomtypes ]
> > > ;type mass charge ptype sigma epsilon
> > > CH 12.01100 0.420 A 3.80000e-01 3.26944e-01
> > > CLCL3 35.45300 -0.140 A 3.47000e-01
> 1.25604e+00
> > >
> > > [ atomtypes ]
> > > ;name at.num mass charge ptype c6
> c12
> > > CH 6 13.01100 0.000 A 0.39376E-02
> > 0.11856E-06
> > > CL3 17 35.45300 0.000 A
> > 0.87710E-02 0.15300E-06
> > >
> > >
> > > The sigma and epsilon LJ-parameters is very good to discribe
> > chloroform
> > > box in the molecular topology of user contributions.
> > >
> >
> http://www.gromacs.org/component/option,com_docman/task,cat_view/gid,36/dir,DESC/order,name/limit,5/limitstart,10/
> > <
> http://www.gromacs.org/component/option,com_docman/task,cat_view/gid,36/dir,DESC/order,name/limit,5/limitstart,10/
> >
> > >
> > <
> http://www.gromacs.org/component/option,com_docman/task,cat_view/gid,36/dir,DESC/order,name/limit,5/limitstart,10/
> > <
> http://www.gromacs.org/component/option,com_docman/task,cat_view/gid,36/dir,DESC/order,name/limit,5/limitstart,10/
> >>
> > > But when I use C6&C12 LJ-parameters I can not get equilibrium and
> the
> > > moleculars sticked together.
> > >
> > cd src/contrib/
> > make sigeps
> > manual chap. 4
> > check combination rules
> >
> > > Thanks in advance.
> > >
> > > --
> > > Sincerely yours,
> > > James Jianzhang
> > >
> > >
> > >
> > >
> >
> ------------------------------------------------------------------------
> > >
> > > _______________________________________________
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> >
> >
> > --
> > David.
> >
> ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se
> > <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> > <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
> >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
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> >
> >
> >
> >
> > --
> > Sincerely yours,
> > James Jianzhang
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > 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!
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> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at 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
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>
--
Sincerely yours,
James Jianzhang
Department of Mechanical and Chemical Engineering
North Carolina Agricultural and Technical State University
1601 East Market Street
Greensboro, NC 27411
jzhang at ncat.edu or james.zhangj at gmail.com
http://www.ncat.edu/~jzhang
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