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

Claus Valka lastexile7gr at yahoo.de
Wed Dec 12 09:47:33 CET 2007

Dear Sir,

I would try to be more precise.

example1 mdp file:
rlist = (greater or equal to rvdw)
vdw-type = Switch

Between the value 5.56 and 8.9 gromacs uses cubic

example2 mdp file:

vdw-type = Cut-off
rvdw-switch=0 (this value here should be irrelevant)

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:
...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,

--- 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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