[gmx-users] charmm 27 gromacs version mdp query

[ram bio]

Dear Gromacs Users,

I have a protein lipid bilayer system built using Gromacs 4.5.4 and
charmm27 FF. Now, i want to equilibrate the built in system using NPT
ensemble, for that i have made to mdp files and as i have never used
Charmm, I am not sure whether the mdp files i am using are correct, so I
want to know your any suggestions and corrections in my mdp files (below),
so that i can use the corrected mdp file to simulate the system.

*1st mdp file :*

title                  = Bilayer-500
cpp                    = /lib/cpp
constraints            = all-bonds
integrator             = md; A leap-frog algorithm for integrating Newton's
equations of motion
dt                     = 0.002
tinit                  = 0; starting time for your run (only makes sense
for integrators md, sd and bd)
nsteps                 = 2000000 ; 4 ns
nstcomm                = 1
nstxout                = 5000
nstvout                = 5000
nstfout                = 0
nstxtcout              = 500
xtc_precision          = 1000
nstlog                 = 500
nstenergy              = 500
nstlist                = 10
; long range interactions
coulombtype            = PME
rlist                  = 1.2; neighborlist cut-off
rcoulomb               = 1.2; Coulomb cut-off
rvdw                   = 1.2; VdW cut-off
fourierspacing         = 0.12; The maximum grid spacing for the FFT grid
when using PPPM or PME
pme_order              = 4
; Berendsen temperature coupling is on in two groups
Tcoupl                 = berendsen
tau_t                  = 0.1   0.1 0.1
tc-grps                = protein POP  SOL
ref_t                  = 303     303  303
; Energy monitoring
energygrps             = protein POP SOL
; pressure coupling is on
Pcoupl                 = berendsen
pcoupltype             = semiisotropic
tau_p                  = 1.0    1.0
compressibility        = 4.5e-5 4.5e-5
ref_p                  = 1.0    1.0

gen_vel                = yes
gen_temp               = 303.0
gen_seed               = 478905

2nd mdp file:
title                  = Bilayer-500
cpp                    = /lib/cpp
constraints            = all-bonds
integrator             = md; A leap-frog algorithm for integrating Newton's
equations of motion
dt                     = 0.002
tinit                  = 0; starting time for your run (only makes sense
for integrators md, sd and bd)
nsteps                 = 2000000 ; 4 ns
nstcomm                = 1
nstxout                = 5000
nstvout                = 5000
nstfout                = 0
nstxtcout              = 500
xtc_precision          = 1000
nstlog                 = 500
nstenergy              = 500
nstlist                = 10
; long range interactions
rlist           = 1.2
rlistlong       = 1.4
rcoulomb        = 1.2
rvdw            = 1.0
vdwtype         = switch
rvdw_switch     = 0.8
coulombtype     = PME
pme_order       = 4
fourierspacing  = 0.16

; Berendsen temperature coupling is on in two groups
Tcoupl                 = berendsen
tau_t                  = 0.1   0.1 0.1
tc-grps                = protein POP  SOL
ref_t                  = 303     303  303
; Energy monitoring
energygrps             = protein POP SOL
; pressure coupling is on
Pcoupl                 = berendsen
pcoupltype             = semiisotropic
tau_p                  = 1.0    1.0
compressibility        = 4.5e-5 4.5e-5
ref_p                  = 1.0    1.0

gen_vel                = yes
gen_temp               = 303.0
gen_seed               = 478905

Your help is highly appreciated.

Thanks

Pramod
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