Dear gmx users,
I tried to apply distance restraints to my system, but I found that it
failed because the distance between the restraints atoms in the last frame
is bigger than what we want. Here are the parameters for distance
restraints in the topology file:
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
8 192 1 0 1 0.0 0.3 0.4 2.5
18 203 1 0 1 0.0 0.3 0.4 2.5
20 205 1 0 1 0.0 0.3 0.4 2.5
and also I tried this (added four other distance restraints in the same two
groups):
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
7 193 1 0 1 0.0 0.3 0.4 2.5
8 192 1 0 1 0.0 0.3 0.4 2.5
11 195 1 0 1 0.0 0.3 0.4 2.5
18 202 1 0 1 0.0 0.3 0.4 2.5
20 202 1 0 1 0.0 0.3 0.4 2.5
18 203 1 0 1 0.0 0.3 0.4 2.5
20 205 1 0 1 0.0 0.3 0.4 2.5
I am sure that the atom numbers are right.
And the following lines are the mdp file I used:
title = PDXN of Abeta in H2O
;cpp = /lib/cpp ; prepocessor of the current machine
define = ;-DPOSRES
integrator = md ; molecular dynamics algorithm
tinit = 0.0 ; start time and timestep in ps
dt = 0.002 ; time step in ps
nsteps = 1000000 ; number of steps for 1000 ns run
emtol = 100 ; convergence criterion
emstep = 0.05 ; intial step size
nstlist = 0 ; step frequency for updating neighbour list
ns_type = simple ;grid ; method for neighbour searching (?)
nstxout = 5000 ; frequency for writing coords to output
.trr file
nstvout = 0 ; frequency for writing velocities to
output...should be same as nstxout
nstfout = 0 ; frequency for writing forces to output
nstlog = 5000 ; frequency for writing energies to log
file
nstenergy = 5000 ; frequency for writing energies to energy
file
nstxtcout = 5000 ; frequency for writing coords to xtc traj
xtc_grps = system ; group(s) whose coords are to be written
in xtc traj
energygrps = system ; group(s) whose energy is to be written in
energy file
;distance restraints
disre = simple
disre_fc = 20000 ; for the force, I tried 3000, 6000, 10000 and
15000, but all the tests failed
disre_mixed = yes
disre_weighting = equal
disre_tau = 10
nstdisreout = 100
;
comm_mode = angular
nstcomm = 10
comm_grps = system
;
pbc = no ;xyz ; use pbc
rlist = 0 ;1.4 ; cutoff lengths (nm)
epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range
or DC of reaction field
niter = 100 ; Some thingies for future use
fourierspacing = 0.16
fourier_nx = 30
fourier_ny = 30
fourier_nz = 30
coulombtype = Cut-off ; truncation for minimisation, with
large cutoff
rcoulomb = 0 ;1.4
rcoulomb-switch = 0
vdw-type = Cut-off ; truncation for minimisation, with
large cutoff
rvdw-switch = 0
rvdw = 0 ; 1.4 ; cut-off lengths
;pme_order = 6 ; EWALD/PME/PPPM parameters
;ewald_rtol = 1e-05
;ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
Free energy control stuff
free_energy = yes
init_lambda = 0.0
delta_lambda = 0
sc_alpha =0.5
sc-power =1.0
sc-sigma = 0.3
;nstcomm = 0 ; number of steps for centre of mass
motion removal (in vacuo only!)
Tcoupl = V-rescale ;Berendsen
tc_grps = system ;Other Water_and_ions
tau_t = 0.5 ; 0.5
ref_t = 300 ; 300
Pcoupl = no
;Pcoupltype = Isotropic
;tau_p = 1.0 1.0 1.0
;ref_p = 1.0 1.0 1.0
;compressibility = 4.5e-5 ; compressibility
annealing = no ; SIMULATED ANNEALING CONTROL
;zero_temp_time = 0 ; Time at which temperature should be zero
(ps)
gen_vel = yes
gen_temp = 300
gen_seed = -1
constraints = all-bonds ; OPTIONS FOR BOND CONSTRAINTS
constraint-algorithm = Lincs ; Type of constraint algorithm
lincs_order = 4 ; Highest order in the expansion of the
constraint coupling matrix
lincs_warnangle = 30 ; Lincs will write a warning to the stderr
if in one step a bond rotates
; over more degrees than
unconstrained-start = no ; Do not constrain the start configuration
;Shake-SOR = no ; Use successive overrelaxation to reduce
the number of shake iterations
;shake-tol = 1e-04 ; Relative tolerance of shake
morse = no ; Convert harmonic bonds to morse potentials
Could someone help me to figure it out? Is there some parameter that I
missed to add? Thanks very much~
--
Best Regards,
Qinghua
--
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