On 8/18/12 5:59 PM, Andrew DeYoung wrote:
Hi,
If you have time, I have some questions about the neighbor list and cut-off
values.
I am running NVT simulations with coulombtype = PME and vdwtype = cut-off.
I have specified equal neighbor search, vdw, and Coulomb cut-offs: rlist =
1.5 nm, rvdw = 1.5 nm, rcoulomb = 1.5 nm. Is it a good idea to use rlist =
rvdw = rcoulomb? (I typically use the default value of nstlist: nstlist =
10.)
According to the manual
(http://manual.gromacs.org/current/online/mdp_opt.html#vdw), using vdwtype =
cut-off means that neighbor searching will be performed using a twin-range
approach. rvdw must be greater than or equal to rlist, rvdw >= rlist; in my
case, I am using rvdw = rlist. Is this a good idea?
Refer to the PDF manual for greater detail. Since a single interaction range
neighbor searching method is a special case of the twin-range method, one is, in
a sense, always using a twin-range method. The online manual leaves this
somewhat ambiguous but the print manual contains a much better explanation.
The cutoff values should be dictated by the force field you're applying. I've
never seen a force field in Gromacs that should be used with 1.5-nm cutoffs, but
perhaps you're using something that is non-standard.
Section 4.6.3 of the manual describes. Of course, in the neighbor list,
"all interaction pairs within rlist are stored." But "interactions between
pairs that do not fall within rlist but do fall within max(rcoulomb,rvdw)
are computed during neighbor searching." Does this statement imply that I
should use rvdw > rlist, rather than rvdw = rlist?
Again, this is dictated by the parameterization of the force field. You're
presupposing a solution to a problem that does not necessarily exist.
However, there is no "grace distance" in Gromacs
(http://lists.gromacs.org/pipermail/gmx-users/2004-January/008831.html).
According to Berk Hess:
"There is no 'grace distance' in Gromacs. A pair of atoms is put in the
neighborlist if the centers of geometry of the charge groups they belong to
are inside the cut-off distance. Thus some atom pairs might not interact
while they are inside the cut-off distance, while other atom pairs might
interact while they are outside the cut-off distance. These charge groups
are important for simulations with cut-off electrostatics as they reduce the
cut-off noise significantly. With shiftted electrostatics or PME charge
groups are only important for performance reasons."
The above paragraph seems to imply that I should use rvdw = rlist. The
above paragraph seems to say that since, unlike other MD codes that do not
use charge groups, in Gromacs there is really no need for a "grace distance"
-- because the use of charge groups, rather than atoms, in a sense has a
"bult-in" grace distance. The charge groups are unlikely to move much
between neighbor list updates every nstlist steps.
Most force fields use single-atom charge groups, so the distinction between
"charge group pair" and "atom pair" is dependent upon the force field.
So, my question is, am I at risk for artifacts if I use rvdw = rlist?
Should I instead use rvdw >= rlist?
Again, it's up to the force field parameterization. If you're using settings
for which your parameter set was derived, then you're not introducing any *new*
artifacts, but any that exist within the original derivation would be preserved.
Whether or not that's acceptable is up to you and anyone who critiques the
work. Without more information about the force field you're using, it's hard to
say whether anything you're doing is inherently "right" or not, because, as
stated above, 1.5-nm cutoffs are incorrect for any of the standard force fields
that come with Gromacs.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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