On 11/29/12 10:40 AM, escajarro wrote:
This is my mdp file for energy minimization:
constraints = none
; integration parameters
integrator = l-bfgs
dt = 0.00
nsteps = 15000
; center of mass removal
nstcomm = 10
comm_mode = Linear
; neighbour searching
nstlist = 1
ns_type = grid
pbc = xyz
rlist = 1.4
; electrostatics
coulombtype = Reaction-Field-zero
rcoulomb = 1.1
epsilon_r = 1.0
epsilon_rf = 0.0
; van der Waals interactions
vdwtype = cut-off
rvdw = 1.4
DispCorr = EnerPres
; Ewald parameters
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-6
optimize_fft = yes
; energy minimization
emtol = 0.1
emstep = 0.01
And this is the one for MD
constraints = none
; integration parameters
integrator = md
tinit = 0
dt = 0.001
nsteps = 10000000
;init_step = 0
comm_mode = linear
nstcomm = 10
; output control
nstxout = 10000
nstvout = 10000
nstfout = 0
nstlog = 10000
energygrps = hexane-UA ethanol
; neigbour searching
nstlist = 1
ns_type = grid
pbc = xyz
rlist = 1.4
; electrostatics
coulombtype = Reaction-Field-zero
rcoulomb = 1.1
epsilon_r = 1.0
epsilon_rf = 0.0
; van der Waals interactions
vdwtype = cut-off
rvdw = 1.4
DispCorr = EnerPres
; Ewald parameters
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-6
optimize_fft = yes
; Generate velocities
gen_vel = yes
gen_temp = 298.0
gen_seed = -1
To use as the starting configuration the last configuration of the
minimization, I used the confout.gro file of the minimization as the input
conf.gro for MD. I also tried using the traj.trr file generated after
minimization with the grompp option -t for MD. I used the same top and ndx
files in both simulations.
The .mdp files look reasonable enough, though setting nstlist = 1 during MD will
cost you a lot of performance. A value in the 5-10 range should suffice.
Do other ensembles work, like NVT? Does a smaller timestep affect stability?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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