[gmx-users] NVT ensemble

[fsaadedi at staffmail.ed.ac.uk]

Dear fellow users,


I have been trying to equilibrate my DOPC bilayer using an NVT ensemble for
100ps.  Unfortunately the equilibration crashes after just 1.5ps.  It crashes
because several bonds rotated more than 30 degrees.  I have tried contraining
my bonds all-bonds, hbonds and none with no effect.  If anyone has any
suggestions I would appreciate them.

Thank you for your time

Farid



I include my nvt.mdp file


; PREPROCESSING
title                  = DOPC
cpp                    = /lib/cpp
include                = -I.

; RUN CONTROL
integrator             = md
tinit                  = 0
dt                     = 0.002
nsteps                 = 50000
nstcomm                = 1

; LANGEVIN DYNAMICS

; ENERGY MINIMIZATION
;emtol                  = 1000.0
;emstep                 = 0.01
;nstcgsteep             = 1000

; SHELL MOLECULAR DYNAMICS

; OUTPUT CONTROL
nstxout                = 100 ; co-ordinates
nstvout                = 0   ; velocities
nstfout                = 0   ; forces
nstlog                 = 0
nstenergy              = 50
nstxtcout              = 100

; NEIGHBOR SEARCHING
nstlist                = 10
ns_type                = grid
pbc                    = xyz
rlist                  = 1.0

; ELECTROSTATICS AND VDW
coulombtype            = Cut-off
rcoulomb               = 1.2      ; electrostatic cutoff in nm
epsilon_r              = 100.0
vdwtype                = Cut-off
rvdw                   = 1.0      ; vdw/lj cutoff in nm
dispcorr               = no

; TEMPERATURE COUPLING
tcoupl                 = nose-hoover
tau_t                  = 0.01 0.01 0.01 0.01;0.1 0.1 0.1
ref_t                  = 300 300 300 300
tc_grps                = OLA OLB DPC SOL

; PRESSURE COUPLING
coupl                 = berendsen
coupltype             = semi-isotropic
;tau_p                  = 5.0 5.0 5.0 ; was 5.0 5.0 5.0
;compressibility        = 4.5e-5 4.5e-5 4.5e-5
;ref_p                  = 1.0 1.0 1.0

; SIMULATED ANNEALING
annealing              = no
zero_temp_time         = 100

; VELOCITY GENERATION
gen_vel                = yes
gen_temp               = 300.0


;BONDS
constraints            = hbonds ; none/all-bonds
;constraint_algorithm   = shake
morse                  = no

;Relative tolerance of shake
shake-tol             = 0.0001

; ENERGY GROUP EXCLUSIONS

; NMR REFINEMENT

; FREE ENERGY PERTUBATION
free_energy             = no

; NON-EQULIBRIUM MD

; ELECTRIC FIELDS


_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.