I wonder whether increasing the surface tension parameter
sa-surface-tension might solve the problem with the protein unfolding.
Thanks,
Gianluca
On Mon, 4 Nov 2013, Gianluca Interlandi wrote:
Hi Justin,
We are using infinite cutoffs (all vs all). Here is the mdp file for the
heating (please note that -DPOSRES is commented out) and the time step is 1
fs:
; 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 =
; 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 = 0
; 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 = 0
; ns algorithm (simple or grid) =
ns_type = simple
; Periodic boundary conditions: xyz or no =
pbc = no
; nblist cut-off =
rlist = 0
;rlistlong = 1.8
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 0
; 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 = 0
; 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
; Time constant (ps) and reference temperature (K) =
tau_t = 0.1
ref_t = 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
; Number of time points to use for specifying annealing in each group
annealing_npoints = 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
; 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
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 5
gen_seed = 173529
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
;constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; 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
On Mon, 4 Nov 2013, Justin Lemkul wrote:
On 11/4/13 2:25 PM, Gianluca Interlandi wrote:
Dear Mark,
Sorry for replying to an older thread. We are trying to perform implicit
solvent
simulations of protein G with CHARMM27 in gromacs. We are trying to
trouble
shoot why the protein unfolds after already 2 ns of dynamics. We use
simulated
annealing for the heating with 1 fs time step. The thermostat is v_rescale
and
OBC is the GBSA algorithm. Do you have any suggestions what we could
improve?
You mention using a sub-fs time step for the equilibration. Do you still
use
LINCS? Do you use simulated annealing to heat up the system or do you just
apply
position restraints to the heavy atoms?
A complete .mdp file would be helpful. Are you using finite cutoffs?
-Justin
Thanks,
Gianluca
On Wed, 28 Aug 2013, Mark Abraham wrote:
It can be. Lack of explicit degrees of freedom of solvent can make
achieving equipartition tricky. With CHARMM27 and virtual sites in
implicit
solvent, I have sometimes found it necessary to use a sub-femtosecond
time
step at the start of equilibration, even where there were no atomic
clashes. Maybe the system was just unlucky with generating velocities,
though :-)
Mark
On Aug 28, 2013 7:16 AM, "Gianluca Interlandi"
<gianl...@u.washington.edu>
wrote:
How important is it to do gentle heating (using simulated annealing)
with
GBSA? Often with explicit water it is enough to perform some
equilibration
with positional restraints. Would it be enough to do the same with
implicit
solvent?
Thanks,
Gianluca
------------------------------**-----------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.**washington.edu/<http://artemide.bioeng.washington.edu/>
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
------------------------------**-----------------------
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-----------------------------------------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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-----------------------------------------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
-----------------------------------------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
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