[gmx-users] Vacuum simulation in GMX 5 (Justin Lemkul)

[Justin Lemkul]

On 5/7/15 8:04 AM, Eudes Fileti wrote:
> Hi Justin, this is my mdp options.

I'm guessing you missed my reply from yesterday:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097266.html

-Justin

> thanks
> eef
>
> ; Run control
> define                   = -DPOSRES
> integrator               = sd       ; Langevin dynamics
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 5000000    ; 100 ps
> nstcomm                  = 100
> ; Output control
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 100
> nstenergy                = 100
> nstxout-compressed       = 0
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme            = verlet
> nstlist                  = 20
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.2
> ; Electrostatics
> coulombtype              = cut-off
> rcoulomb                 = 1.2
> ; van der Waals
> vdwtype                  = cutoff
> vdw-modifier             = force-switch
> rvdw-switch              = 1.0
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                  = no
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> tcoupl                   = v-rescale
> nsttcouple               = -1
> nh-chain-length          = 10
> print-nose-hoover-chain-variables = no
> ; Groups to couple separately
> tc-grps                  = system
> ; Time constant (ps) and reference temperature (K)
> tau-t                    = 0.1
> ref-t                    = 323
> ; pressure coupling
> Pcoupl                   = no
> Pcoupltype               = isotropic
> nstpcouple               = -1
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau-p                    = 2.0
> compressibility          = 4.5e-5
> ref-p                    = 1.0
> ; Scaling of reference coordinates, No, All or COM
> refcoord-scaling         = com
>
> ; Free energy control stuff
> free_energy              = yes
> init_lambda_state        = 0
> delta_lambda             = 0
> calc_lambda_neighbors    = 1        ; only immediate neighboring windows
> vdw_lambdas             = 0.00 0.00 0.00 0....... .70 0.75 0.80 0.85 0.90
> 0.95 1.00
> coul_lambdas              = 0.00 0.05 0.10 0........1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00
> ; Options for the decoupling
> sc-alpha                 = 0.5
> sc-coul                  = no       ; linear interpolation of Coulomb (none
> in this case)
> sc-power                 = 1.0
> sc-sigma                 = 0.3
> couple-moltype           = Pept      ; name of moleculet ype to decouple
> couple-lambda0           = vdw-q      ; only van der Waals interactions
> couple-lambda1           = none     ; turn off everything, in this case
> only vdW
> couple-intramol          = yes
> nstdhdl                  = 10
> ; Generate velocities to start
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = -1
> ; 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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