Hi all,

I am running CGMD simulation of a membrane protein in DPPC with Martini FF.

I just want to check if these mdp files are correct. I would appreciate if you take a look and tell me if there is something wrong or missing.

<*minimization.mdp*>
integrator       =  steep
dt               =  0.02
nsteps           =  500
nstxout          =  0
nstvout          =  0
nstlog           =  100
nstxtcout        =  100
xtc-precision    =  10
rlist            =  1.4
coulombtype      =  shift
rcoulomb         =  1.2
epsilon_r        =  15
vdw-type         =  shift
rvdw-switch      =  0.9
rvdw             =  1.2
tcoupl           =  v-rescale
tc-grps          =  Protein DPPC W_Ion
tau-t            =  1.0 1.0 1.0
ref-t            =  300 300 300
define          = -DPOSRES

<*equilibration.mdp*>
dt               =  0.02
nsteps           =  25000
nstxout          =  0
nstvout          =  0
nstlog           =  100
nstxtcout        =  100
xtc-precision    =  100
rlist            =  1.4
coulombtype      =  shift
rcoulomb         =  1.2
epsilon_r        =  15
vdw-type         =  shift
rvdw-switch      =  0.9
rvdw             =  1.2
tcoupl           =  v-rescale
tc-grps          =  Protein DPPC W_Ion
tau-t            =  1.0 1.0 1.0
ref-t            =  300 300 300
Pcoupl           =  parrinello-rahman
Pcoupltype       =  semiisotropic
tau-p            =  12.0 12.0
compressibility  =  3e-4 3e-4
ref-p            =  1.0 1.0
refcoord_scaling =  all

<*md_2us.mdp*>
dt               =  0.02
nsteps           =  100000000
nstxout          =  0
nstvout          =  0
nstlog           =  10000
nstxtcout        =  1000
xtc-precision    =  100
rlist            =  1.4
coulombtype      =  shift
rcoulomb         =  1.2
epsilon_r        =  15
vdw-type         =  shift
rvdw-switch      =  0.9
rvdw             =  1.2
tcoupl           =  v-rescale
tc-grps          =  Protein DPPC W_Ion
tau-t            =  1.0 1.0 1.0
ref-t            =  300 300 300
Pcoupl           =  parrinello-rahman
Pcoupltype       =  semiisotropic
tau-p            =  12.0 12.0
compressibility  =  3e-4 3e-4
ref-p            =  1.0 1.0

Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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