[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units
t.piggot at bristol.ac.uk
Mon Jul 16 19:07:32 CEST 2007
If i understand correctly then rlist is the short range cutoff inside which
the forces on the atoms are calculated every step (and the neighbour list is
updated every nstlist steps).
If you specify a value of rvdw or rcoulomb larger than rlist then the
forces on the atoms between rlist and rvdw/rcoulomb are re-calculated only
nstlist steps (and again the neighbour list is updated every nstlist
steps). However it does not make sense to do this for rcoulomb when using
PME because if you did this then forces inside rlist and outside rcoulomb
would be updated every step but for outside rlist and inside rcoulomb only
updated every nstlist steps, so for PME rcoulomb should equal rlist.
I think this is correct but i am sure someone will tell me if it is not.
--On Monday, July 16, 2007 06:56:41 -0400 Frankie Montenegro
<frankie.montenegro at gmail.com> wrote:
> 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.
> [gmx-users] again, rlist vs rvdw vs rcoulomb and something about energy
> 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)
> 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.
> 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
> 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,
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t.piggot at bristol.ac.uk
University of Bristol, UK.
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