[gmx-users] Basic GROMACS questions

[Simone Bolognini]

Thank you Justin. Your answer was very helpful. Since I tries like 3-4
GROMACS tutorials I wanted to try to simulate dynamics with my own
parameters. I'm trying to simulate the chicken prion protein fragment 1U3M
using gromos53a6 as force field. I followed the typical protocol for
dynamics (vacuum minimization, addition of solvent and neutralization, in
solvent minimization, position restrained dynamics and production). Here
are my .mdp files for the various tasks:

;VACUUM MINIMIZATION
define = -DFLEXIBLE
integrator         = cg
emtol = 50
nstcgsteep = 1000
nsteps = -1

nstenergy = 1
energygrps = System

nstlist = 1
nstype = simple
pbc = no

coulombtype = cut-off
vdwtype = cut-off
rvdw = 1
rlist = 1
rcoulomb = 1

actually I could have used PME electrostatics with pbc here
emtol is set in such a way that convergence is really reached (I tried with
different values and looked at the convergence of the potential energy)


;SOLVENT MINIMIZATION
define = -DFLEXIBLE

integrator = cg
emtol = 500
nstcgsteep = 1000
nsteps = -1

nstenergy = 1
energygrps = System

nstlist = 10
nstype = grid
pbc = xyz

coulombtype = PME
vdwtype = cut-off
rvdw = 1
rlist = 1
rcoulomb = 1
fourierspacing = 0.15
pme-order = 4
ewald-rtol = 1e-5
optimize-fft = yes


;PRD
define = -DPOSRES
constraints     = all-bonds
constraint_algorithm = LINCS

integrator = md-vv-avek
dt = 0.002
nsteps = 50000
nstcomm = 10

nstenergy = 10
nstxout = 500
nstxtcout      = 500
nstvout = 5000
nstfout = 0
nstlog = 10

nstlist = 10
nstype = grid
pbc = xyz

coulombtype = PME
vdwtype = cut-off
rvdw = 1.
rlist = 1.
rcoulomb = 1.
fourierspacing = 0.16
pme-order = 4
ewald-rtol = 1e-5
optimize-fft = yes

tcoupl       = Berendsen
tau_t       = 0.5  0.5
tc_grps       = protein non-protein
ref_t       = 300 300
nsttcouple = 1

pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord_scaling = all
nstpcouple = 1

gen_vel = yes
gen_temp = 300
gen_seed = -1


;PRODUCTION
constraints     = all-bonds
constraint_algorithm = lincs
lincs_iter = 1
lincs_order = 4

integrator = md-vv-avek
dt       = 0.002
nsteps = 500000
nstcomm = 10

nstenergy = 10
nstxout = 1000
nstxtcout = 1000
nstvout = 1000
nstlog = 1000

nstlist = 5
nstype = grid
pbc = xyz

coulombtype = PME
vdwtype       = cut-off
rvdw = 1.0
rlist = 1.0
rcoulomb = 1.0
fourierspacing = 0.16
pme-order = 4
ewald-rtol = 1e-5
optimize-fft = yes

tcoupl       = nose-hoover  ; nose-hoover extended ensamble
tau_t       = 0.5 0.5   ; relaxation-time
tc_grps       = protein non-protein
ref_t       = 300 300

pcoupl       = Parrinello-Rahman
pcoupltype      = isotropic
tau_p       = 2.0
compressibility = 4.5e-5
ref_p       = 1.0
refcoord_scaling = all
gen_vel      = no


Thank you again for your help!!!