Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 22 19:32:55 CET 2010
nishap.patel at utoronto.ca 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,
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> nishap.patel at utoronto.ca wrote:
>>> 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
>> 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.
>>> 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
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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
> Telephone: 416-978-1536
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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