I am trying to perform protein MD simulation at the air/water interface. Every time I submit the mdrun it gives me LINCS WARNING. I have energy minimized the structure for 10,000 steps.
My **.mdp file is as follows.
define = -DPOSRES_ON
integrator = md
dt = 0.001
nsteps = 25000
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstcalcenergy = 100
nstenergy = 1000
;
;cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
vdwtype = Cut-off
;vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
;
ewald-geometry = 3dc ;slab geometry
pbc = xyz
;
tcoupl = V-rescale
tc_grps = Protein NA CL SOL ligand
tau_t = 0.1 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300 300
;
pcoupl = no
pcoupltype = semi-isotropic
tau_p = 5.0 5.0
compressibility = 4.5e-5 0 ;0 for z-direction due to vaccum slab
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 100
comm_mode = linear
;
refcoord_scaling = com
sa-surface-tension = 0
Thanks the reply, but my protein is very big (1023 amino acid). So, can we perform air-water interphase MD for such a big system?
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