raghu...@bcpindia.org wrote:
Dear Users and Developers
I am trying to execute md_pull.mdp {given below} on a small molecule
embedded at the core of lipid bilayer. I have tried to modify the
md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling. I
encounter LINCS warning (1000) after about 100-110 ps of the simulation
resulting in termination of mdrun. This occurs when the small molecule
is near the polar heads. I understand the system is exploding.
I have minimized the system, followed by anneal to 323K then nvt and npt
after which I perform the md_pull. How can I soften the core {as
mentioned in the errors on www.gromacs.org} or any other alternative is
there adding lincs warning to mdp file {I am not aware}
"Soft core" is a mechanism by which Lennard-Jones interactions are modified
while doing decoupling/annihilation calculations. This point is not relevant here.
I see that you're restraining the lipids in some way. Which atoms are
restrained? In which directions? Why are you restraining them? I would assume
that as a molecule is pulled through your membrane, any artificial forces that
work against one another would cause instability.
-Justin
Following is the md_pull.mdp file as modified;
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
title = Umbrella pulling simulation
define = -DPOSRES_DPPC
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 100000 ; 200 ps
nstcomm = 1
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Nose-Hoover
tc_grps = TPF DPPC SOL
tau_t = 0.1 0.1 0.1
ref_t = 323 323 323
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of x-y box
vectors, independent z
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, x-y, z
(in bar)
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = DPPC
pull_group1 = TPF
pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Please help me
Thanks N Regards
Raghuvir
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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