Vitaly,
your are right in principle but for "real" systems long-range LJ
interactions do matter a lot.
In addition Justin reference the following is a good example of
the effect of treatment of long-range interaction:
Anezo et al. J. Phys. Chem. B 2003, 107, 9424-9433
XAvier.
On Mar 25, 2010, at 11:46 AM, Vitaly V. Chaban wrote:
XAvier,
You should probably know that E(LJ)(r)->0 at r->2.5*sigma. This is a
result of pure mathematical analysis. If all the sigmas in your system
are less than 0.4 nm, then after r=1.0 nm, the energy is very close to
zero.
All your below statement are correct but they do not address the
problem if E(LJ)->0 at R(cutoff). This was the only hint I posted
before.
Vitaly
On Thu, Mar 25, 2010 at 12:37 PM, XAvier Periole <[email protected]>
wrote:
the development of biomolecular force fields in general have tough
the community that cutoff values are important parameters for any
force field, this is true for both Elec and vdW interactions.
The example of a bilayer was the most obvious to me when thinking
of the effect of the vdW cutoff. The balance between the Elec and vdW
is determinant to the properties of the bilayer. No particular atom-
pair
in mind, though.
It important not to give the wrong impression to people new in the
field. The literature is full of reports of cutoff artefacts ...
On Mar 25, 2010, at 9:29 AM, Vitaly V. Chaban wrote:
On Thu, Mar 25, 2010 at 12:45 AM, XAvier Periole
<[email protected]> wrote:
On Mar 24, 2010, at 10:58 PM, Vitaly V. Chaban wrote:
Hi,
I want to test different values of cutoff for vdw. However, in
the list
someone said cutoff = 0.9 for vdw was used for paramaterizing of
Gromos
force field, other values would cause error, and also there was
someone
saying that cutoff for vdw should be set to 1.4. Can >someone
make this
question clear? Thanks a lot.
The common rule for all FFs is to set the LJ-cutoff around
2.5*sigma(LJ12-6). In fact, you'll get about 0.9 nm for the most
objects. I see nothing terrible if you use, say, 1.4 nm just
because
the difference will be negligible.
Where is that coming from? This is so wrong!
From the properties of LJ12-6 curve.
Just test it. :)
I've you ever tried that on a lipid bilayer?
My interests are a bit shifted from bilayers. What concrete atom
pair
will cause the problem in your example?
Who could ever say (whatever force field) a vdW cutoff of 0.9/1.4
nm
is no difference?
--
Dr. Vitaly Chaban
--
--
Dr. Vitaly Chaban
http://chaban.at.ua
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