[email protected] wrote:
I see what you mean, so say if I am doing RDF, the values beyond 9A
would be bogus?
To a large extent, probably, but I don't think that I can say that absolutely
without context. For example, you've only shown us rvdw, what about rcoulomb?
If it is longer for some reason, then this value will also influence the RDF.
Long-range electrostatics (i.e., PME) may have some effect as well, but I don't
really have much detailed experience in doing that sort of thing.
There is a nice section in the manual about RDF calculation, as well as an
example RDF plot for SPC water that should give you an idea of what to expect,
in general.
-Justin
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Hello,
I wanted to know, if say my box is 30A (cubic) and if I set my
cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that
mean, the simulation will cut-0ff at 9A? Should I be changing that
to 1.5nm (to get half the box cut-off)? I am a little confused about
that.
Setting rvdw = 0.9 means that van der Waals interactions beyond 0.9 nm
are zero. It has no effect on, for example, Coulombic interactions.
Most force fields have defined cutoffs that should be used in order to
be consistent with the original derivation of the parameter set, so it
is generally inadvisable to make ad hoc changes to the cutoffs in order
to meet some arbitrary criterion. The minimum image convention
specifies that your longest cutoff must always be less than half the
smallest box vector. If you set up a system with a cutoff equal to
exactly one half of a box vector, if that box vector decreases even
slightly (i.e., under the influence of pressure coupling), then you
will be calculating spurious forces.
-Justin
Thanks.
Nisha Patel
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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