Hi all,
I have embedded protein into POPC bilayer, I accomplished energy
minimisation
em.mdp file
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 500
; Energy minimizing stuff
;
emtol = 100
emstep = 0.01
nstcomm = 1.0
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.4
Tcoupl = no
Pcoupl = no
its showed following sentences
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100
Double precision normally gives you higher accuracy.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 104 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -2.2754422e+05
Maximum force = 2.3355256e+03 on atom 913
Norm of force = 9.4749170e+03
gcq#191: "These Gromacs Guys Really Rock" (P.J. Meulenhoff)
So I dont boughter about those sentences because I confirmed in list archives
that I can proceed further steps and moreover em.gro file is fine, so I
went for restrain, here I am getting abnormal POPC structure
means POPC tails are tilting, water molecules structure also disturbed.
Could you please tell me where iam doing mistake?
my pr.mdp filetitle = protein in popc restrained
define = -DPOSRES_protein
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 10000 ; total 50 ps.
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.4
pbc = xyz
; Berendsen temperature coupling is on in three groups
Tcoupl = Berendsen
tc-grps = POPC Protein SOL_CL-
tau_t = 0.1 0.1 0.1
ref_t = 310 310 310
; Anisotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = anisotropic
tau_p = 1.0 1.0 1.0 0 0 0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p = 1.0 1.0 1.0 0 0 0
; Energy monitoring
energygrps = POPC Protein SOL_CL-
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
Thanks in advance.
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