On 11/7/13 11:32 PM, Rajat Desikan wrote:
Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html
Is there any reason not to use their .mdp parameters for a membrane-protein
system? Justin's recommendation is highly valued since I am using his
forcefield. Justin, your comments please
Careful now, it's not "my forcefield." I derived only a very small part of it
:)
To summarize:
Klauda et al., suggest
rlist = 1.0
rlistlong = 1.4
rvdw_switch = 0.8
vdwtype = Switch
coulombtype = pme
DispCorr = EnerPres ;only usefull with reaction-field
and pme or pppm
rcoulomb = 1.0
rcoulomb_switch = 0.0
rvdw = 1.2
Justin's recommendation (per mail above)
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2
The differences between these two sets of run parameters are very small, dealing
mostly with Coulomb and neighbor searching cutoffs. I would suspect that any
difference between simulations run with these two settings would be similarly
small or nonexistent, given that rcoulomb is a bit flexible when using PME. The
value of rlist is rarely mentioned in papers, so it is good that the authors
have provided the actual input file. Previous interpretation of CHARMM usage
generally advised setting rcoulomb = 1.2 to remain consistent with the original
switching/shifting functions. That setting becomes a bit less stringent when
using PME.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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