[gmx-users] Help about Table.xvg

[David van der Spoel]

kun jiao wrote:
> Thanks, David. I look into this file, and I know I need to set vdwtype = 
> user in *.mdp file.
>  But I still don't know how to set [ nonbond_parms ] in force field file,
>  which relate this table.xvg with two atoms type.
> This is my force field file. Could you tell me how to modify it to 
> specify CH3 CH3 interaction as vdw potential in table.xvg
> 
> -----------------------------------------------------------------------
> [ defaults ]
> 1       1
> [ atomtypes ]
> ;name     mass     charge ptype  c6           c12
> ;
>   CH3    14.0000    0.000  A 2.36400e-03 1.59000e-06
> 
> 
> [ nonbond_params ]
>   ; i    j    func    c6           c12
>   CH3   CH3     1 2.36400e-03  1.59000e-06

This is fine with the normal table6_12

> ----------------------------------------------------------------------------------------------
> 
> On 12/1/05, *David van der Spoel* < spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>> wrote:
> 
>     kun jiao wrote:
> 
>      > Dear, Gromacs Community,
>      >     I am a new user of Gromacs. In my project I need to implement a
>      > very complicate vdw potential. I read the gromacs manual which said I
>      > need to prepare a table.xvg file.
>      > But I have no idea how this file looks like, and how to relate it
>     with
>      > top file ( how to specify nonbond_params ). Could anyone give me an
>      > example, such as table.xvg, *.top,  *.itp ?.
> 
> 
>     in share/top you will find 6-12 etc. tables.
>     Basically you need
>     x fc(x) fc"(x) fd(x) fd"(x) fr(x) fr"(x)
>     fc(x) will be multiplied by charges
>     fd(x) by dispersion constant (C6)
>     fr(x) by repulsion constant (C12)
> 
>      > Any suggestion is appreciate:)
>      >
>      > Regards,
>      > Kun
>      >
>      >------------------------------------------------------------------------
> 
>      >
>      >_______________________________________________
>      >gmx-users mailing list
>      >gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>      > http://www.gromacs.org/mailman/listinfo/gmx-users
>      >Please don't post (un)subscribe requests to the list. Use the
>      >www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>      >
> 
> 
>     --
>     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://xray.bmc.uu.se/~spoel
>     ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>     _______________________________________________
>     gmx-users mailing list
>     gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.


-- 
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://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++