[gmx-users] Gentle heating with implicit solvent
Gianluca Interlandi
gianluca at u.washington.edu
Tue Nov 5 18:41:57 CET 2013
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"
>>>> <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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>>>>>
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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
>>
>> ==================================================
>> --
>> 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.
> -----------------------------------------------------
>
-----------------------------------------------------
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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