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

Claus Valka lastexile7gr at yahoo.de
Tue Dec 11 18:04:25 CET 2007


I have searched thoroughly the manual and the gmx
list, yet with no avail. I'm trying to understand how
I will be able to implement to gromacs my system which
is complicated as far as the non bonded interactions
are concerned. 

My system comprises three different types of atoms.
The LJ interactions (non bonded) among them are
divided in two different categories : local and non
The local ones are the interactions of atoms 3 and 4
bonds away and the non local for every combination of
atoms more than 4 bonds away.

1st question: nrescl is equal to 4?

2nd question: in my itp file for the intramolecular
1-4 interactions I have created the [ pairs ] tab in
which I give the 1-4(3bonds apart) and 1-5(4bonds
apart) atoms with their corresponding c6=4*σ^6
and c12=4*σ^12 as follows: 
  [ pairs ]
 ;  ai   aj    funct   c6     c12
   atom1 atom4    1
   atom1 atom5    1
Am I correct?

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.

4th question: I want after 1,45*σ till
2,33*σ to use the cubic spline in such a way that
the LJ potential will go smoothly to zero at
2,33σ. If I use the biggest σ 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 ?

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?

6th question: If I want to use a quintic spline
between 1,45*σ till 2,33*σ(cut-off value)
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 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?

Forgive me for the long list of questions, yet with
what I have to my disposal (mailing list, manual) it
was impossible for me to find a solution.

Yours Sincerely,

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