[gmx-users] (no subject)

[Frankie Montenegro]

Hi guys,

My first question is with regards to the size relationship
between rlist and rvdw/rcoulomb, and consequently the
meaning of rlist.

I found an excellent question on this exact same subject
 posted couple of years ago, but I couldn't find the answer to
 it. I copy parts of the question here, and I would greatly appreciate
some comments. It's rather long, so I tried to cut
 and paste parts of it that are relevant to me.

####################################
Quote:

[gmx-users] again, rlist vs rvdw vs rcoulomb and something about energy groups
m b mic0404 at yahoo.com
Fri Jul 25 04:32:00 CEST 2003


dear all,

I do MD simulations using a cutoff for
both VdW and Coulomb interactions.
I am rather confused about the
parameters used in the input file.
(rlist, rvdw, rcoulomb)

--------------------cut--------------------------------------

Normally I would assume that if one uses
a neighbour list there are (at least) two cutoffs:
One for a sphere around each atom with ALL
(and only) the atoms in this sphere considered when
calculating the energy and the forces on
the primary atom at EACH time step (rvdw,
rcoulomb ?).
A second (larger) cutoff that is used when
calculating the neighbour-list at intervals
of each 10 (or so) time steps (rlist ?)
were of course rlist > rvdw and rcoulomb.

If one uses a switched potential there
is a third cutoff (the onset of the switching
function) that would be shorter than
rvdw and rcoulomb.

this implies: rlist > rvdw,rcoulomb > r*_switch
... in contrast to (part of) the manual, and the
errormsg given by the code.

----------------------cut--------------------------------------

In my calculations I now let
rlist < rvdw, rcoulomb, to evade
the error message that Gromacs gives me
otherwise, but if what I wrote above is true
then the physical implications would
be a bit worrying ...
and if I have rlist = rvdw, rcoulomb
would that not mean that the neighbour list
has to be re-calculated at each time-step
to get consistant results ?

So the question is: is what I wrote above
correct or not ? and if not, what is the
precise meaning of these parameters (rlist,
rvdw, etc)


End of Quote.
####################################

My second question
I am trying to minimize a model binary Lennard-Jones system.
 It is a cubic box, side length 5 sigmas (so, the size is in
 reduced units, sigma=1).I have two atom types, so I followed
 the manual and set sigma_ii = epsilon_ii = 1 for one atom type.
 I set rlist=1, but grompp_d complaines that

          "ERROR: The cut-off length is longer than half
           the shortest box vector or longer than the
           smallest box diagonal element. Increase the
           box size or decrease rlist."

Now, it seems to me that, if sigma_ii = 1, all lengths values in the
mdp file (such as rlist) will be in units of sigma. Am I right
 here? r*=r/sigma=r/1=r, right? If so, why is grompp complaining about
the size which is less then a quarter of the
 box? (At first I thought it is complaining about rlist being too
 small.)

So, in conclusion, I either don't understand:

A) meaning of the size of rlist,

B) conversion to reduced units,

C) quite possibly both.

Here is my potential, if that can be of any help.

PE_ij=sigma_ij^6 * [ 16.0* epsilon_ij / R_ij^6
                          - 12.0 * epsilon_ij * r_ij^2 / R_ij^8
                          - 4.0 * epsilon_ij / r_ij^6 ]
         +sigma_ij^12 * [-28.0 * epsilon_ij / R_ij^12
                             +24.0*epsilon_ij * r_ij ^2/ R_ij^14
                             + 4.0 * epsilon_ij  / r_ij^12 ]

where R_ij= const * sigma_ij
is the cutoff for each of the three interactions.

Thanks for your help,
Frankie