[gmx-users] Constant-Force Pulling of Ubiquitin
Weiwei Tao
wwtao at bu.edu
Tue Oct 29 16:51:21 CET 2013
Hi GMX Users,
I am using Gromacs (Version 4.5.5) to do constant-force pulling of
ubiquitin and it's a implicit model. My mdp file for pulling is shown as
following.
integrator = md
dt = 0.001 ; ps !
nsteps = 500000 ; total 500 ps.
nstxout = 100
nstvout = 100
nstfout = 100
nstlist = 10
nstlog = 100
nstcalcenergy =100
rlist = 5
rvdw = 5
rcoulomb = 5
coulombtype = cut-off
vdwtype = cut-off
table-extension = 5
bd_fric = 0
ld_seed = -1
pbc = no
ns_type = simple
constraints = all-bonds
lincs_order = 4
lincs_iter = 1
lincs-warnangle = 30
Tcoupl = v-rescale
tau_t = 1.0
tc-grps = Protein
ref_t = 300
Pcoupl = no
gen_vel = yes
gen_temp = 300
gen_seed = 173529
comm_mode = Angular
nstcomm =100
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = gbsa
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 5
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension = 2.05016
; Pull code
pull = constant_force
;Center of mass pulling using a linear potential and therefore a constant
force.
pull_geometry = direction
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group1 = Chain_B
pull_group0 = Chain_A
pull_k1 = -500 ; kJ mol^-1 nm^-2
pull_vec1 = 0.0 0.0 1.0
However, after pulling simulation, it turns out the potential of this
system becomes lower rather than higher (from -10000 to -20000). It's very
wired since potential should become larger after pulling.
Here is the notification after g_energy:
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential -20734.5 230 1268.47 -1385.71
(kJ/mol)
You may want to use the -driftcorr flag in order to correct for spurious
drift in the graphs. Note that this is not
a substitute for proper equilibration and sampling! You should select the
temperature in order to obtain fluctuation properties.
I wonder whether there is any problem with my mdp file.
Thank you so much!!
Best,
Vivian
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