[gmx-users] rvdw vs cut-off / different types of non bonded interactions

[Claus Valka]

Dear Sir,

I'm absolutely aware that gromacs uses nm for
distance. The values should be 0.556 and 0.89. I used
them only for reference purposes and I hope that this
didn't cause any misanderstanding so as to point me to
the manual. If this is the case of not understanding
my questions, I deeply appologize.

Yours Sincerely,
Nikos
--- David van der Spoel <spoel at xray.bmc.uu.se>
schrieb:

> 
> 
> On Wed, 12 Dec 2007, Claus Valka wrote:
> 
> > Dear Sir,
> >
> > I would try to be more precise.
> >
> > example1 mdp file:
> > rlist = (greater or equal to rvdw)
> > vdw-type = Switch
> > rvdw-switch=5.56
> > rvdw=8.9
> >
> are you aware that gromacs usues nm for distance?
> 
> you can find the functional form of the shift/switch
> function in the 
> manual.
> 
> > Between the value 5.56 and 8.9 gromacs uses cubic
> > spline?
> >
> > example2 mdp file:
> >
> > rlist=5.56
> > vdw-type = Cut-off
> > rvdw-switch=0 (this value here should be
> irrelevant)
> > rvdw=8.9
> >
> > Gromacs uses cubic spline after the value 8.9 till
> LJ
> > to go to zero?
> >
> > And which is the difference of rlist if someone
> uses
> > vdw-type = Cut-off instead of vdw-type = Switch?
> It
> > would have been nice to have images of these
> options
> > so as to be better understood.
> > Because it is stated in the manual:
> > rlist: (1) [nm]
> > cut-off distance for the short-range neighbor list
> > and also:
> > Switch
> > ...The neighbor search cut-off rlist should be 0.1
> to
> > 0.3 nm LARGER than rvdw...
> > Isn't this a little bit contradictive?
> >
> > As far as twin cutoffs are concerned if we want to
> > find out the total energy of the non bonded
> > interactions we have to add LJ-14 + LJ(SR) +
> LJ(LR)?
> >
> > With tabulated potentials can I use different
> cutoffs
> > for different types of atoms? Judging from your
> answer
> > about system wide cutoffs I understand that even
> > though I might use tabulated potentials, I won't
> be
> > able to use different cutoffs for the different
> types
> > of atoms I have. Am I correct?
> >
> > Yours Sincerely,
> > Nikos
> >
> >
> > --- Mark Abraham <Mark.Abraham at anu.edu.au>
> schrieb:
> >
> >> Claus Valka wrote:
> >>> Hello,
> >>>
> >>
> >>> 3rd question: Which is the difference between
> the
> >>> S(hort)R(ange) LJ and LJ 1-4? For me the short
> >> range
> >>> interactions are the 1-4LJ, yet it seems that
> this
> >> is
> >>> not the case.
> >>
> >> GROMACS uses twin-range cutoffs (see manual), so
> >> LJ-SR is inside the
> >> shorter cutoff, and LJ-LR is outside.
> >>
> >>> 4th question: I want after 1,45*&#963; till
> >>> 2,33*&#963; to use the cubic spline in such a
> way
> >> that
> >>> the LJ potential will go smoothly to zero at
> >>> 2,33&#963;. If I use the biggest &#963; I have,
> >> then
> >>> in the mdp file rvdw-switch=5.56 and rvdw=8.9.
> >> Between
> >>> these two values does the cubic spline work as a
> >>> switch function using vdw-type = Switch ?
> >>
> >> Please find a way to describe your problem with
> >> plain ASCII text.
> >>
> >>> 5th question: Given the above if I use vdw-type
> >>> =Cut-off and rvdw=8.9 then gromacs will use
> cubic
> >>> spline till the LJ will reach zero for a value
> >> greater
> >>> than 8.9, yet to me uknown? If this is not the
> >> case
> >>> how LJ goes to zero with this option?
> >>
> >> I don't understand what you're asking.
> >>
> >>> 6th question: If I want to use a quintic spline
> >>> between 1,45*&#963; till 2,33*&#963;(cut-off
> >> value)
> >>> for the different combination of atoms(they have
> >>> different &#949; and &#963;), then should I use
> a
> >>> tabulated potential? And if I do that which will
> >> be
> >>> the meaning of cutoffs in the mdp file as I
> would
> >> like
> >>> them to be different for each of the different
> >> types
> >>> of atoms I have? Can I use different cut-offs
> for
> >> the
> >>> different types of atoms I have?
> >>
> >> The cut-offs are a system-wide property.
> >>
> >> Mark
> >> _______________________________________________
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> >
> >
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