[gmx-users] position restraint....NEED URGENT HELP

[nikhil damle]

Hey !

My doubt posted few days back still holds. I am trying to simulate the kinase domain in complex with cyclin. when i keep entire complex either position restrained or flexible, MD runs without any errors. But as soon as i keep cyclin position restrained keeping kinase domain flexible, it gives errors. 

Initially it gave LINCS warnings saying fatal error that charged group at atom xxxxxx moved more than distance allowed by DD in direction X. Error persists even if i repeat the same procedure this time equilibrating the system for 150ps instead of usual 40ps. the pdb file obtained after equilibration appears perfect without any breaks.

As suggested by Justin, I also tried to check if my system is blowing up. But when i take co-ordinates of last frame, i get few random fragments having no 3D structure/ interconnections.

Here is .top file that i am using:

title = KD with Cyc PR test run
;warnings = 10
cpp = /usr/bin/cpp
define = -DPOSRES_B ; with DPOSRES it works fine. without any define option also it works fine
constraints = all-bonds
integrator = md
dt = 0.002
nsteps = 5000
nstcomm = 1
comm_mode = Linear
nstxout = 10
nstvout = 10
nstfout = 10
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 2.0
coulombtype = PME
rcoulomb = 2.0; in nm units
vdwtype = cut-off
rvdw = 2.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temp coupling: on
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
; Pressure coupling: on
Pcoupl = parrinello-rahman
tau_p= 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocities
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529


I wish to do MD with increased electrostatic and VdW cut-offs. Chain B is Cyclin and A is kinase domain.

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