[gmx-users] Re: cutoff problem

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 25 12:08:55 CET 2010

Vitaly V. Chaban wrote:
> On Thu, Mar 25, 2010 at 12:45 AM, XAvier Periole <x.periole at rug.nl> 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.
> attr
>>> 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?

The value of rvdw strongly affects properties of lipid bilayers.  It is not 
true, in this case at least, to say that the differences between rvdw = 0.9 and 
1.4 are negligible.  Perhaps in aqueous systems, where Coulombic interactions 
dominate, the effect is minimal, but I can't speak to that directly.  With 
bilayers, from Patra et al. (2003) Biophys. J. 84: 3636-3645:

"Simulations similar to those with rvdw = 1.0 nm have been run with rvdw = 1.4 
nm.  The average area per lipid using PME is reduced by 0.051 nm^2, whereas the 
average areas per lipid for three different cutoffs - rcut = 1.8 nm, 2.0 nm, or 
2.5 nm - are reduced by 0.017, 0.046, and 0.067 nm^2, respectively.  This trend 
is understandable since an increase in rvdw effectively increases the attractive 
interaction between the acyl chains, thus reducing the area per molecule."

The balance of attractive and repulsive forces used in the derivation of the 
force field can indeed be affected by changing these parameters, as is quite 
clear from the statement above.


>>> --
>>> Dr. Vitaly Chaban
>>> --


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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