[gmx-users] dispersion correction and heterogeneous systems

Chris Neale chris.neale at utoronto.ca
Wed Jan 31 01:09:25 CET 2007

Does anybody have any experience with DispCorr=EnerPres and a 
heterogeneous system (e.g. aggregation of detergents to form micelles)? 
What about membranes? Even if it is not a perfect method, is an 
imperfect assumption of homogeneous LJ density beyond the cutoff better 
than entirely ignoring it?

Currently I am using NPT with DispCorr=No. I am working my way toward 
free energy calculations in which I gather that I must use 
DispCorr=EnerPres. However, for simulations that are not intended for 
free energy calculation is DispCorr=No quite acceptable?

I used acrobat to search through all of my downloaded pdf's and have 
tabulated the results below. Although this list contains 14 papers that 
mention the long range dispersion correction (tail correction, cutoff 
correction), that only represents 5% of the papers that I searched 
through, most of them being MD papers. If I had instead searched for 
pressure coupling or PME or some other widely applied method then I am 
sure that the list would have been very much longer.

Papers that apply long range corrections as the best method:
Shirts and Pande, JCP 122, 134508 (2005)
Feller and MacKerrel, Jr. JPC.B, 104, 7510-5 (2000) although I am not 
sure if they applied the correction during the MD or in post-processing

Papers that apply long range corrections as the best method (parameter 
Horn, Swope, and Pitera, JCP, 120, 9665-78 (2004) use it in their TIP4P-Ew
Ryckaert and Bellemans, 1978 "Molecular Dynamics of Liquid Alkanes"
Jorgensen, Madura, and Swenson, JACS, 106, 6638-46 (1984)
Jorgensen, Maxwell, and Tirado-Rives, JACS, 118, 11225-36 (1996)
Kaminski et al, JPC.B, 105, 6474-87 (2001)

Papers that apply long range corrections as one possible option:
Lindahl, Hess, and van der Spoel, J Mol. Model, 7, 306-17 (2001) use 
them in one of the benchmarks
Anezo et al, J.Phys.Chem.B, 107, 9424-33 (2003) use them as one option 
in a  parameter spectrum for lipids
van der Spoel, Maaren, and Berendsen, JCP, 108, 10220-30 (1998) apply it 
but only in the presence of a reaction field
Price and Brooks JCP, 121, 10096-103 (2004) have a TIP3P-Ew and a 
TIP3P-PME/LRC (LRC=long range correction for LJ)

Papers that mention long range corrections but do not use them:
van der Spoel and Maaren, JCTC, 2, 1-11 (2006) do not apply it (but it 
is mentioned) although perhaps this is because that paper was in direct 
response to a previous study.
Bembenek, JCP, 124, 014709 (2006) mentions it but does not use it

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