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gel phase dppc bilayer mdp parameters
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14 years 4 days ago #354
by adwait
gel phase dppc bilayer mdp parameters was created by adwait
Hi All,
I am trying to simulate gel phase of a dppc bilayer using martini force field, using
Prof. Marrink's 2005 paper "Simulation of gel phase formation and melting in lipid bilayers
using a coarse grained model" as a reference. I am currently using standard martini parameters
for the simulation given at martini website.
My system consists of 512 dppc and has 8000 CG waters In the paper anisotropic coupling has
been used, so i wanted to know what kind of values were input for it?
Also was the compressibility changed from 3e-5 to some other value or was it kept the
same?
Does it make a difference if the topology used is ver 2.1 rather than 2.0?
some parameter values that i am using are the same as in mdp on website except for these:
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 283 283
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0
compressibility = 3e-5
ref_p = 1.0
Thanks for your help in advance.
-Adwait
Project Assistant,
Institute of Mathematical Sciences,
Chennai,
India.
I am trying to simulate gel phase of a dppc bilayer using martini force field, using
Prof. Marrink's 2005 paper "Simulation of gel phase formation and melting in lipid bilayers
using a coarse grained model" as a reference. I am currently using standard martini parameters
for the simulation given at martini website.
My system consists of 512 dppc and has 8000 CG waters In the paper anisotropic coupling has
been used, so i wanted to know what kind of values were input for it?
Also was the compressibility changed from 3e-5 to some other value or was it kept the
same?
Does it make a difference if the topology used is ver 2.1 rather than 2.0?
some parameter values that i am using are the same as in mdp on website except for these:
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 283 283
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0
compressibility = 3e-5
ref_p = 1.0
Thanks for your help in advance.
-Adwait
Project Assistant,
Institute of Mathematical Sciences,
Chennai,
India.
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