[gmx-users] cut-off

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Fri Jan 22 19:20:06 CET 2010

I see what you mean, so say if I am doing RDF, the values beyond 9A  
would be bogus?

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> nishap.patel at utoronto.ca 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
> 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
Telephone: 416-978-1536

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