[gmx-users] rvdw vs cut-off / different types of non bonded interactions
David van der Spoel
spoel at xray.bmc.uu.se
Wed Dec 12 09:51:54 CET 2007
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
are you aware that gromacs usues nm for distance?
you can find the functional form of the shift/switch function in the
> 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:
>>> 3rd question: Which is the difference between the
>>> S(hort)R(ange) LJ and LJ 1-4? For me the short
>>> interactions are the 1-4LJ, yet it seems that this
>>> 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*σ till
>>> 2,33*σ to use the cubic spline in such a way
>>> the LJ potential will go smoothly to zero at
>>> 2,33σ. If I use the biggest σ I have,
>>> in the mdp file rvdw-switch=5.56 and rvdw=8.9.
>>> 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
>>> than 8.9, yet to me uknown? If this is not the
>>> 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*σ till 2,33*σ(cut-off
>>> for the different combination of atoms(they have
>>> different ε and σ), then should I use a
>>> tabulated potential? And if I do that which will
>>> the meaning of cutoffs in the mdp file as I would
>>> them to be different for each of the different
>>> of atoms I have? Can I use different cut-offs for
>>> different types of atoms I have?
>> The cut-offs are a system-wide property.
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