[gmx-users] Issue in Steep descent minimization (Free energy calculation)

[Justin Lemkul]

On 1/14/16 4:02 AM, Live King wrote:
> Hi everyone,
>
>
> I know this issue has been addressed several times but I couldn't find the
> solution for my problem. So, I had to ask here.
>
> I am trying to calculate free energy using martini forcefield. My system
> has water, DPPC bilayer and membrane protein embedded in it. After steepest
> descent minimization I get the following note/warning.
>
>
>
>
> *"Stepsize too small, or no change in energy.Converged to machine
> precision,but not to the requested precision Fmax < 100 " *
>
>
> I know it means my structure has clashes or my mdp options are not
> adequate. I tried to played with all the suggested parameters before. If

That's not what the message means.

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

-Justin

> more suggestions will be highly appreciated.My mdp file looks like this :-
>
>
> ; Run control
> integrator               = steep
> nsteps                   = 5000
> ; EM criteria and other stuff
> emtol                    = 100
> emstep                 = 0.01
> niter                     = 20
> nbfgscorr              = 10
> ; Output control
> nstlog                  = 1
> nstenergy             = 1
> ; Neighborsearching and short-range nonbonded interactions
> nstlist                  = 1
> ns_type                  = grid
> pbc                      =  xyz
> rlist                      = 1.2
> ; Electrostatics
> coulombtype           = shift
> rcoulomb                 = 1.2
> rcoulomb_switch          = 0.0
> ; van der Waals
> vdw-type                 = shift
> rvdw-switch              = 0.9
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                  = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> optimize_fft             = no
> ; Temperature and pressure coupling are off during EM
> tcoupl                   = no
> pcoupl                   = no
> ; Free energy control stuff
> free_energy              = yes
> init_lambda              = 0.0
> delta_lambda             = 0
> foreign_lambda           = 0.05
> sc-alpha                 = 1.3
> sc-power                 = 1.0
> sc-sigma                 = 0.47
> couple-moltype           = Protein  ; name of moleculetype to decouple
> couple-lambda0           = vdw-q      ; only van der Waals interactions
> couple-lambda1           = none
> couple-intramol          = yes
> nstdhdl                  = 10
> ; Generate velocities to start
> gen_vel                  = no
> ; options for bonds
> constraints              = h-bonds  ; we only have C-H bonds here
> ; Type of constraint algorithm
> constraint-algorithm     = lincs
> ; Do not constrain the starting configuration
> continuation             = no
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order              = 12
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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