[gmx-users] Implicit solvent, Simulated annealing, Remove motion of center of mass
ElisaHarrison
e.harrison.fsu at gmail.com
Fri Jan 3 00:38:33 CET 2014
Hi all,
The system I'm working with is Protein G (ID: 1PG) with a graphene surface
using Implicit Solvent.
I perform an energy minimization using steepest descent with 1000 steps and
0.001 ps time step. Then I use simulation annealing for 200ps to heat the
system to 300K.
After heating, the protein lays on it's side and then spins around about 1.5
times.
I include "comm-mode = linear" and "comm-grps = protein" in the heating mdp
file to stop the protein from moving linearly (and relatively fast) along
the surface, but it is unsettling that the protein is still spinning.
Does anyone have any ideas on how to best remove the motion of the centers
of mass (linear and angular) in a protein/surface system with implicit
solvent?
Thank you.
Below is my heating mdp file..
;
; File 'mdout_pr.mdp' was generated
periodic-molecules = yes
; VARIOUS PREPROCESSING OPTIONS =
title =
cpp = /lib/cpp
include =
;define = -DPOSRES
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0
dt = 0.001
nsteps = 200000
; mode for center of mass motion removal =
comm-mode = linear
; number of steps for center of mass motion removal =
nstcomm = 1
; group(s) for center of mass motion removal =
comm-grps = protein
; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
;bd-temp = 300
bd-fric = 0
ld_seed = 1993
; IMPLICIT SOLVENT OPTIONS =
implicit-solvent = GBSA
gb-algorithm = OBC
rgbradii = 2.1
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol = 0.000001
emstep = 0.01
; Max number of iterations in relax_shells =
niter = 100
; Step size (1/ps^2) for minimization of flexible constraints =
fcstep = 0
; Frequency of steepest descents steps when doing CG =
nstcgsteep = 1000
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 100
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps =
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = simple
; Periodic boundary conditions: xyz or no =
;pbc = no
; nblist cut-off =
rlist = 2.1
rlistlong = 2.3
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 2.1
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 1
; Method for doing Van der Waals =
vdw-type = Cut-off
; cut-off lengths =
rvdw_switch = 0
rvdw = 2.1
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.1
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
Tcoupl = V-rescale
; Groups to couple separately =
tc_grps = Protein Non-Protein
; Time constant (ps) and reference temperature (K) =
tau_t = 0.1 0.1
ref_t = 300 300
; Pressure coupling =
Pcoupl = no
Pcoupltype = isotropic
refcoord_scaling = All
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; SIMULATED ANNEALING CONTROL =
annealing = single single
; Number of time points to use for specifying annealing in each group
annealing_npoints = 21 21
; List of times at the annealing points for each group
annealing_time = 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140
150 160 170 180 190 200 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150
160 170 180 190 200
; Temp. at each annealing point, for each group
annealing_temp = 5 30 30 60 60 90 90 120 120 150 150 180 180 210
210 240 240 270 270 300 300 5 30 30 60 60 90 90 120 120 150 150 180 180 210
210 240 240 270 270 300 300
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 5
gen_seed = 173529
; OPTIONS FOR BONDS =
constraints = all-bonds
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
;unconstrained_start = no
;continuation = yes
; Use successive overrelaxation to reduce the number of shake iterations =
Shake-SOR = no
; Relative tolerance of shake =
shake_tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
; Convert harmonic bonds to morse potentials =
morse = no
; NMR refinement stuff =
; Distance restraints type: No, Simple or Ensemble =
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
=
disre_weighting = Equal
; Use sqrt of the time averaged times the instantaneous violation =
disre_mixed = no
disre_fc = 1000
disre_tau = 1.25
; Output frequency for pair distances to energy file =
nstdisreout = 100
; Orientation restraints: No or Yes =
orire = no
; Orientation restraints force constant and tau for time averaging =
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) to energy file =
nstorireout = 100
; Free energy control stuff =
free_energy = no
init_lambda = 0
delta_lambda = 0
sc-alpha = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff =
cos-acceleration = 0
--
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