[gmx-users] can Gromacs 4.5 use VDW long range correction? IN the mannual, In this version, GROMACS always uses a cut-off radius for the Lennard-Jones interactions

[MD]

Hi All,
 
I have to use the long range correction for VDW, in fact i used cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we can get 65 dyn. The .mdp i used are as follow, I really need to know how to get a surface tension of 69.5 dyn for TIP4P/2005 water model. Becasue my surpervisor is so picky, everything should be perfacet, and i feel really tired by his way. Any comment will be greatly appreciated,
 
The main parameter is
 

coulombtype = PME

rcoulomb-switch = 0

rcoulomb = 1.4

; 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 = 3.8

; Apply long range dispersion corrections for Energy and Pressure

DispCorr = EnerPres

; Extension of the potential lookup tables beyond the cut-off

table-extension = 1

; Spacing for the PME/PPPM FFT grid

fourierspacing = 0.12

 

 

 

 

The full .mdp are as follow,

 

 

;

; File 'mdout.mdp' was generated

; By user: spoel (291)

; On host: chagall

; At date: Mon Dec 15 13:13:06 2003

;

; VARIOUS PREPROCESSING OPTIONS

title = Yo

cpp = /usr/bin/cpp

include =

define =

; RUN CONTROL PARAMETERS

integrator = md

; Start time and timestep in ps

tinit = 0

dt = 0.001

nsteps = 400000

; For exact run continuation or redoing part of a run

init_step = 0

; 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-fric = 0

ld-seed = 1993

; ENERGY MINIMIZATION OPTIONS

; Force tolerance and initial step-size

; Max number of iterations in relax_shells

niter = 20

　

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)

nstxout = 5000

nstvout = 8000

nstfout = 8000

; Checkpointing helps you continue after crashes

nstcheckpoint = 1000

; Output frequency for energies to log file and energy file

nstlog = 5000

nstenergy = 5000

; Output frequency and precision for xtc file

nstxtcout = 500

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 = 5

; ns algorithm (simple or grid)

ns_type = grid

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc = xyz

; nblist cut-off

rlist = 1.4

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype = PME

rcoulomb-switch = 0

rcoulomb = 1.4

; 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 = 3.8

; Apply long range dispersion corrections for Energy and Pressure

DispCorr = EnerPres

; Extension of the potential lookup tables beyond the cut-off

table-extension = 1

; Spacing for the PME/PPPM FFT grid

fourierspacing = 0.12

; 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

; GENERALIZED BORN ELECTROSTATICS

; Algorithm for calculating Born radii

gb_algorithm = Still

; Frequency of calculating the Born radii inside rlist

nstgbradii = 1

; Cutoff for Born radii calculation; the contribution from atoms

; between rlist and rgbradii is updated every nstlist steps

rgbradii = 2

; Salt concentration in M for Generalized Born models

gb_saltconc = 0

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)

implicit_solvent = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS

; Temperature coupling

Tcoupl = v-rescale

; Groups to couple separately

tc-grps = System

; Time constant (ps) and reference temperature (K)

tau_t = 0.1

ref_t = 300

; Pressure coupling

Pcoupl = no

Pcoupltype = isotropic

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau_p = 1

compressibility = 4.5e-5

ref_p = 1.0

; Random seed for Andersen thermostat

andersen_seed = 815131

; SIMULATED ANNEALING

; Type of annealing for each temperature group (no/single/periodic)

annealing = no

; Number of time points to use for specifying annealing in each group

annealing_npoints =

; List of times at the annealing points for each group

annealing_time =

; Temp. at each annealing point, for each group.

annealing_temp =

; GENERATE VELOCITIES FOR STARTUP RUN

gen_vel = yes

gen_temp = 300

gen_seed = 1993

; 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

; Number of iterations in the final step of LINCS. 1 is fine for

; normal simulations, but use 2 to conserve energy in NVE runs.

; For energy minimization with constraints it should be 4 to 8.

lincs-iter = 1

; 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

; ENERGY GROUP EXCLUSIONS

; Pairs of energy groups for which all non-bonded interactions are excluded

energygrp_excl =

; NMR refinement stuff

; Distance restraints type: No, Simple or Ensemble

disre = No

; Force weighting of pairs in one distance restraint: Conservative or Equal

disre-weighting = Conservative

; Use sqrt of the time averaged times the instantaneous violation

disre-mixed = no

disre-fc = 1000

disre-tau = 0

; Output frequency for pair distances to energy file

nstdisreout = 100

; Orientation restraints: No or Yes

orire = no

; Orientation restraints force constant and tau for time averaging

orire-fc = 0

orire-tau = 0

orire-fitgrp =

; Output frequency for trace(SD) to energy file

nstorireout = 100

; Dihedral angle restraints: No, Simple or Ensemble

dihre = No

dihre-fc = 1000

dihre-tau = 0

; Output frequency for dihedral values to energy file

nstdihreout = 100

; Free energy control stuff

free-energy = no

init-lambda = 0

delta-lambda = 0

sc-alpha = 0

sc-sigma = 0.3

; Non-equilibrium MD stuff

acc-grps =

accelerate =

freezegrps =

freezedim =

cos-acceleration = 0

; Electric fields

; Format is number of terms (int) and for all terms an amplitude (real)

; and a phase angle (real)

E-x =

E-xt =

E-y =

E-yt =

E-z =

E-zt =

; User defined thingies

user1-grps =

user2-grps =

userint1 = 0

userint2 = 0

userint3 = 0

userint4 = 0

userreal1 = 0

userreal2 = 0

userreal3 = 0

userreal4 = 0

 
 
The
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