atomistic vs. coarse grained simulations
DESCRIPTION
Atomistic vs. Coarse Grained Simulations. all atoms vs. four-to-one mapping long range vs. short range interactions only quantitative vs. semi-quantitative slow (ns) vs. fast (ms). 1 coarse grained water 4 atomistic water. =. - PowerPoint PPT PresentationTRANSCRIPT
Atomistic vs. Coarse Grained Simulations
all atoms vs. four-to-one mappinglong range vs. short range interactions only quantitative vs. semi-quantitative slow (ns) vs. fast (ms)
1 coarse grained water
4 atomistic water
atomistic coarse grained
composition:1600 DPPC250000 H2O
15 ns 50 ns 100 ns
180 ns 250 ns150 ns
1 ns 5 ns0 ns
cell size: 20x20x20 nm
simulation time:250 ns
Aggregation into a DPPC bilayer – coarse grained model
starting structure (t=0 ns)
Surrounding water
Aggregation of DPPC into vesiclescomposition:1600 DPPC1000000 H2O
cell size: 30x30x30 nm
simulation time:100 ns
0 ns random 5 ns worms 10 ns bicelle
60 ns cup20 ns bicelle 80 ns vesicle
LAMELLAR
STALK
HEMIFUSION
FUSION PORERHOMBIC
CUBIC HEXAGONAL
Lamellar to Hexagonal Transition for DOPE at low hydrationin agreement with experiment (Rand etal)
t = 0ns t = 20 ns t = 100 nsT=280 -> 320K stalk formation hexagonal phase
t = 20 ns t = 100 ns stalk formation hexagonal phase
Folding Transition States in Proteins
In collaboration with the group of Chris Dobson in Cambridge we have looked at transition states in the folding of SH3 domains.
Objective: To evaluate the folding propensity of proposed transition states (TS) of the a-spectrin
SH3 domain using molecular dynamics (MD) simulations with an explicit representation of the solvent.
Some of the proposed transition states fold other do not.
InitNative
run 1
Configuration 3Configuration 4
run 2
Configuration 2
Examples showing the native state, a proposed transition state and results of 2 independent folding simulations.
Foldingsuccessful
Foldingunsuccessful
Status of our contribution:
1. Trajectories of the simulations mentioned above can be made available on request2. While we have not appointed anyone specifically on the project we are in the
process of advertising.3. Our aim is to specifically appoint a person focusing on code development who could interact with those groups involved in methods development and exploit
our preexisting simulations..