[gmx-users] Re: Is there a way to use diffrent scaling factors for 1-4 interaction? (David)

[David]

On Sun, 2005-11-06 at 09:10 +0800, Xiaobing Feng wrote:
>  Thanks David,
> 
>     The LJ 1-4 interaction can be modified in [pairs] or [pairtypes] sections.
>   I need to use different scaling factors for two 1-4 Coulomb interaction. Can we
>   do this using [pairtypes]?  I checked a few force field files, they all used
>   two values (c6, c12) or (cs6, cs12), I guess only the LJ 1-4 interaction was
>   modified. 
>     I managed to convert my force field from DLPOLY to GROMACS. I used nrexcl=2
>   to include all 1-4 interaction, also I set gen_pairs=yes, fudgeLJ=-1, fudgeQQ=-0.383
>    and in [pairs] I specified a 1-4 atom pairs. This way, two kinds of 1-4 interactions
>    can have different scaling factors (one is 1.0, the other is 0.617) for Coulomb 
>     interaction. It's not a general way, I don't know how to do it if it needs to 
>    use two different Coulomb scaling factors, like 0.6 and 0.8. 
This is difficult indeed. One way would be to add a virtual particle on
the position of the real particle that has part of the charge. You would
then have 1-4 interactions between the "real" particles only and not
between the virtual particles, but it requires manual topology
processing.

> 
>     Thanks very much
> 
>         Xiaobing
> > 
> > 
> > ------------------------------
> > 
> > Message: 3
> > Date: Sat, 05 Nov 2005 07:49:15 +0100
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] Is there a way to use diffrent scaling
> > 	factors for	1-4 interaction?
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID:
> > 	<1131173355.4538.3.camel at 217-208-143-88-o1123.tbon.telia.com>
> > Content-Type: text/plain; charset=UTF-8
> > 
> > On Sat, 2005-11-05 at 13:42 +0800, Xiaobing Feng wrote:
> > > Dear gmx-users,
> > > 
> > >     I'm converting a force field from DLPOLY to GROMACS.
> > >   There are two different 1-4 interactions, one has full 1-4 LJ and Coulomb 
> > >    interaction, the one has scaling factor 0.0 and 0.617 for 1-4 LJ and Coulomb
> > >    interaction, respectively.  Is there a way in GROMACS in which we can
> > >     use different scaling factors for different 1-4 interactions?
> > By specifying a complete matrix of pairtypes
> > 
> > > 
> > >      Many thanks,
> > > 
> > >       Xiaobing
> > > 
> > > 
> > > 	
> > > 
> > > 	
> 
> 
> 
> 	
> 
> 	
> 		
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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    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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