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

[Claus Valka]

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

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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