[gmx-users] Gentle heating with implicit solvent
Gianluca Interlandi
gianluca at u.washington.edu
Mon Nov 4 23:58:33 CET 2013
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" <gianluca at 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 gianluca at 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
>>>> ------------------------------**-----------------------
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
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>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
> --
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at 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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