[gmx-users] dispersion correction and heterogeneous systems
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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