[gmx-users] Advice on the .mdp parameters for CG system with PW using PME

[shivangi nangia]

Hello Gromcas Users,

I need advise for the following mdp file, are these parameters sensible for
my system.

I want to use PME for electrostatics for the CG system.


I am simulating a systems containing POPC, small peptide (21 amino acids),
Polarizable water and ions.

System size: 25766 cg beads
Box size: 9.54013   9.54013  20.00000

;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;

; VARIOUS PREPROCESSING OPTIONS =
title                    = Martini input for MD

; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.

integrator               = md
; start time and timestep in ps
tinit                    = 0.0
dt                       = 0.020
nsteps                   = 80000000
; number of steps for center of mass motion removal =
nstcomm                  = 10
comm-grps                =

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 500000
nstvout                  = 500000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 1000
nstenergy                = 1000
; Output frequency and precision for xtc file =
nstxtcout                = 80000
xtc_precision            = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =

; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.4

; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.

; Method for doing electrostatics =
coulombtype              = PME
rcoulomb                 = 1.4
coulomb-modifier         = Potential-shift-Verlet
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 2.5
; Method for doing Van der Waals =
vdw_type                 = Shift
; cut-off lengths        =
rvdw                     = 1.3
vdw-modifier             = Potential-shift-Verlet
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.

; Temperature coupling   =
tcoupl                   = V-rescale
; Groups to couple separately =
tc-grps                  = Protein Lipid W_ION
; Time constant (ps) and reference temperature (K) =
tau_t                    = 1.0 1.0 1.0
ref_t                    = 323 323 323
; Pressure coupling      =
Pcoupl                   = parrinello-rahman
Pcoupltype               = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 20.0 20.0 20.0
compressibility          = 3e-5 3e-5 3e-5
ref_p                    = 1.0 1.0 1.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = no
;gen_temp                 = 310
gen_temp                 = 323
gen_seed                 = 44933668

; OPTIONS FOR BONDS     =
constraints              = none
; Type of constraint algorithm =
constraint_algorithm     = Lincs
; Do not constrain the start configuration =
unconstrained_start      = no
; Relative tolerance of shake =
shake_tol                = 0.0001
; 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          = 90
;
; for polarizable water sometimes Lincs warnings appear for no apparent
reason
; with a warnangle of 90 this is largely avoided

Thanks so much in advance

sxn