On 8/24/13 11:11 PM, Gianluca Interlandi wrote:
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2
I'm confused about the difference between rlist and rlistlong. I am planning to
also setup an implicit solvent simulation with GBSA and CHARMM-FF. Would this
make sense?
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0
rcoulomb = 1.2
vdw-type = Switch
rvdw_switch = 1.0
rvdw = 1.2
Implicit solvent simulations are a special case, and the cutoffs used are
generally different than in explicit solvent. In fact, I would be willing to
bet that the settings above would lead to unstable structures. Note that you
should not use shifted electrostatics, as they produce significant artifacts,
and the fact that you'd be shifting over the entire range (0 to 1.2 nm) is a
very bad idea, indeed.
With implicit solvent, literature often refers to longer cutoffs, on the order
of 2.0 nm. In my hands, such simulations have never worked. Perfectly stable
proteins unfold and energy drifts badly. The only stable way I have found to
run GBSA simulations is using the all-vs-all approach:
pbc = no
ns_type = simple
rvdw = 0
rcoulomb = 0
rlist = 0
nstlist = 0
Note that the use of zero cutoffs does not mean that interactions are not
calculated; just the opposite - all interactions are calculated.
-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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