[gmx-users] Van der waals types

[Mark Abraham]

On 11/04/12, Chrisostomos Batistakis <tomyvanbatis at gmail.com> wrote:

> Dear Mark
> 
> Many thanks for your responces.
> 
> Yes, of course I have seen that. But what I am asking is if when using vdw-type=cut-off  the potential is shifted acoording to the following equation:
> 
> VLJ=V(r)-V(rc) for r<rc 

 
No. It's cut off - discontinuous and probably fattening. It's equation 4.23 with r_1 = r_c 
 
Mark 

> 
> 
> 
> Regards, Chrysostomos
> 
> 
> On Wed, Apr 11, 2012 at 1:01 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> 
> 
> > 
> > 
> >  
> >  
> > On 11/04/12, Chrisostomos Batistakis <tomyvanbatis at gmail.com> wrote: 
> > 
> > 
> > > Dear Mark
> > > 
> > > I have already checked both sections but I don't understand.. That's why I am asking for help :-)
> > 
> >  
> > 
> > Then you'll have seen that by construction the shifted potential is zero above the cutoff. The question of truncation does not arise.
> > 
> >  
> > Mark
> > 
> > 
> > 
> >  
> > 
> > > 
> > > 
> > > On Wed, Apr 11, 2012 at 12:18 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > > 
> > > 
> > > > 
> > > > 
> > > > 
> > > > On 11/04/12, Chrisostomos Batistakis <tomyvanbatis at gmail.com> wrote:
> > > > 
> > > > > 
> > > > > Dear all
> > > > > 
> > > > > I am looking in the manual but I don't understand...
> > > > > 
> > > > > When using vdw-type =cut-off in the .mdp file, is the LJ potential only truncated in the cut-off distance rc,  or is it also shifted in order to avoid discontinuity when rij=rc ?
> > > > > 
> > > > > If no, how can I have a shifted and truncated LJ potential?
> > > > > 
> > > > 
> > > >  
> > > > 
> > > > 
> > > > Please check out the manual. Sections 4.1 and 7.3.11 come to mind.
> > > > 
> > > >  
> > > > Mark 
> > > > 
> > > > --
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> > 
> >  
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> > 
> > 
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