Hey everybody.
I'm still trying to biuld up a bulk of 2CLJ-molecules (ethane). I just wanna
use fixed connections in-between the CH3-"atoms" and no eletrostatics during
the simulation. I posted my .itp-file several times along my .top-file and my
used .mdp-file. Though the simulation runs fine I'm unhappy with the results,
cause pressure is higher than I expect it to be.
Since Mark told me, I'm not simulating fixed connections I'd like to ask if
ANYBODY could help me with that.
Thanks in advance
Nicolas
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[ moleculetype ]
; name nrexcl
ethane 1
[ atoms ]
; nr type resnr residu atom cgnr charge
1 CH3 1 ETH ET1 1 0.000
2 CH3 1 ETH ET2 2 0.000
[ bonds ]
; ai aj funct
1 2 5
[ constraints ]
; i j type lenght
1 2 1 0.2345
;
Preprocessing-------------------------------------------------------------------------------------------------------------------------------------------
title = Energy Minimization ; redundant,so whatever
comes to your mind
cpp = /usr/bin/cpp ; your preprocessor
;include = /usr/local/gromacs/share/gromacs/top ; directories
to include in your topology
;define = ; for defines in your topology file
;
; Run
Control---------------------------------------------------------------------------------------------------------------------------------------------
integrator = md ; what you wanna do. md
(moleculardynamics),steep (energyminimization), sd, md, cg, l-bfgs, nm, tpi,...
tinit = 0 ; starting time for your run
dt = 0.00333 ; time step for the integration
nsteps = 30000 ; maximum number of steps to integrate
;init_step = ; the starting step {t=tinit +dt*(init_step
+i)}
comm_mode = None ; removal of center of mass movement
;nstcomm = ; frequency of that removal
;comm_grps = ; what groups are considered for removal
;
; Langevin
Dynamics---------------------------------------------------------------------------------------------------------------------------------------
;bd_fric = ; brownian dynamics friction coefficient
;ld_seed = ; used to initialize random generator for
thermal noise for stochastic and Brownian dynamics
;
; Energy
Minimization-------------------------------------------------------------------------------------------------------------------------------------
;emtol = 1 ; the minimization is converged when the
maximum force is smaller than this value
;emstep = 0.01 ; initial step-size
;nstcgsteep = ; frequency of performing 1 steepest descent
step while doing conjugate gradient energy minimization
;nbfgscorr = ; Number of correction steps to use for L-BFGS
minimization. A higher number is more accurate, but slower
;
; Shell Molecular
Dynamics--------------------------------------------------------------------------------------------------------------------------------
;emtol = ; the minimization is converged when the maximum
force is smaller than this value. shell-md: < 1 , em < 10
;niter = ; maximum number of iterations for optimizing
the shell positions and the flexible constraints
;fcstep = ; the step size for optimizing the flexible
constraints
;
; Output
Control------------------------------------------------------------------------------------------------------------------------------------------
nstxout = 10000 ; frequency to write coordinates to output
trajectory file, the last coordinates are always written
nstvout = 10000 ; frequency to write velocities to output
trajectory, the last velocities are always written
;nstfout = ; frequency to write forces to output
trajectory
;nstlog = 5000 ; frequency to write energies to log file,
the last energies are always written
;nstenergy = 250 ; frequency to write energies to energy
file, the last energies are always written
;nstxtcout = 250 ; frequency to write coordinates to xtc
trajectory
;xtc_percision = ; precision to write to xtc trajectory
;xtc_grps = Protein ; group(s) to write to xtc trajectory,
default the whole system is written (if nstxtcout is larger than zero)
;energygrps = Protein SOL ; group(s) to write to energy file
;
; Neighbor
Searching--------------------------------------------------------------------------------------------------------------------------------------
nstlist = 1 ; Frequency to update the neighbor list. When
this is 0, the neighbor list is made only once
ns_type = grid ; grid or simple (grid for large systems)
pbc = xyz ; periodic boundary conditions, xyz (every
direction), no (no pbc)
rlist = 1.75 ; cut-off distance for the short-range
neighbor list
;
;
Electrostatics------------------------------------------------------------------------------------------------------------------------------------------
coulombtype = cut-off ; other: Ewald, PME, PPPM,
Reaction-Field, Generalized-RF, RF-nec, Shift, Encad-Shift, Switch, User,
PME-User
;rcoulomb_switch = ; where to start switching the Coulomb
potential
rcoulomb = 0 ; distance for the Coulomb cut-off
;epsilon_r = ; The relative dielectric constant. A
value of 0 means infinity
;epsilon_rf = ; The relative dielectric constant of
the reaction field. A value of 0 means infinity
;
;
VdW-----------------------------------------------------------------------------------------------------------------------------------------------------
vdwtype = Cut-off ; Cut-off, Shift, Switch,
Encad-Shift, User
;rvdw_switch = ; where to start switching the LJ
potential
rvdw = 1.75 ; distance for the LJ or Buckingham
cut-off
DispCorr = EnerPres ; Dispersion Correction : no, EnerPres,
Ener
;
;
Tables--------------------------------------------------------------------------------------------------------------------------------------------------
;table-extension = ; Extension of the non-bonded potential
lookup tables beyond the largest cut-off distance
;energygrp_table = ; When user tables are used for
electrostatics and/or VdW
;
;
Ewald---------------------------------------------------------------------------------------------------------------------------------------------------
;fourierspacing = ; The maximum grid spacing for the FFT grid when
using PPPM or PME
;fourier_nx = ; Highest magnitude of wave vectors in reciprocal
space when using Ewald
;pme_order = ; Interpolation order for PME
;ewald_rtol = ; The relative strength of the Ewald-shifted direct
potential at the cutoff is given by ewald_rtol
;ewald_geometry = ; The geometry to use for Ewald summations
;epsilon_surface = ; This controls the dipole correction to the Ewald
summation in 3d
;optimize_fft = ; Calculate the optimal FFT plan for the grid at
startup : yes, no
;
; Temperature
Coupling------------------------------------------------------------------------------------------------------------------------------------
tcoupl = Berendsen ; no, Berendsen, Nose-Hoover
tc-grps = ETH ; groups to couple separately to
temperature bath
tau_t = 0.00333 ; time constant for coupling (one for
each group in tc_grps), 0 means no temperature coupling
ref_t = 183 ; reference temperature for coupling
(one for each group in tc_grps)
;
; Pressure
Coupling---------------------------------------------------------------------------------------------------------------------------------------
Pcoupl = no ; no, Berendson, Parinello-Rahman
;pcoupltype = ; isotropic, semiisotropic,
anisotropic, surface-tension
;tau_p = 1.0 ; time constant for coupling
;compressibility = 4.5e-5 ; compressibility (NOTE: this is now
really in bar-1) For water at 1 atm and 300 K the compressibility is 4.5e-5
;ref_p = 1.0 ; reference pressure for coupling
;
; Simulated
Annealing-------------------------------------------------------------------------------------------------------------------------------------
annealing = single ; no, single, periodic
annealing_npoints = 4 ; A list with the number of
annealing reference/control points used for each temperature group
annealing_time = 0 18 26 83 ; List of times at the annealing
reference/control points for each group
annealing_temp = 238 238 183 183 ; List of temperatures at the
annealing reference/control points for each group
;
; Example: Assume you have two temperature groups, set the group selections to
annealing = single periodic, the number of points of each group to
; annealing_npoints = 3 4, the times to annealing_time = 0 3 6 0 2 4 6 and
finally temperatures to annealing_temp = 298 280 270 298 320 320 298. The
; first group will be coupled to 298K at 0ps, but the reference temperature
will drop linearly to reach 280K at 3ps, and then linearly between 280K
; and 270K from 3ps to 6ps. After this is stays constant, at 270K. The second
group is coupled to 298K at 0ps, it increases linearly to 320K at 2ps,
; where it stays constant until 4ps. Between 4ps and 6ps it decreases to 298K,
and then it starts over with the same pattern again, i.e. rising
; linearly from 298K to 320K between 6ps and 8ps. Check the summary printed by
grompp if you are unsure.
;
; Velocity
Generation-------------------------------------------------------------------------------------------------------------------------------------
gen_vel = yes ; Generate velocities according to a
Maxwell distribution at temperature gen_temp [K], yes or no
gen_temp = 183 ; temperature for Maxwell distribution
gen_seed = 100000 ; used to initialize random generator
for random velocities
;
;
Bonds---------------------------------------------------------------------------------------------------------------------------------------------------
constraints = none ; none, hbonds, all-bonds, h-angles,
all-angles
constraint_algorithm = lincs ; lincs, shake
unconstrained_start = no ; no, yes, apply constraints to the
start configuration and reset shells
;shake_tol = ; relative tolerance for shake
;lincs_order = ; Highest order in the expansion of the
constraint coupling matrix
;lincs_iter = ; Number of iterations to correct for
rotational lengthening in Lincs
;lincs_warnangle = ; maximum angle that a bond can rotate
before Lincs will complain
morse = no ; yes, no, bonds are represented by a
Morse potential
;
; Energy Group
Exclusions---------------------------------------------------------------------------------------------------------------------------------
;energygrp_excl = ; Pairs of energy groups for which all
non-bonded interactions are excluded
;
; NMR
Refinement------------------------------------------------------------------------------------------------------------------------------------------
;disre = ; no, simple, ensemble, distance restraints
;disre_weighting = ; conservative, equal
;disre_mixed = ; no, yes
;disre_fc = ; force constant for distance restraints, which
is multiplied by a (possibly) different factor for each restraint
;disre_tau = ; time constant for distance restraints running
average
;nstdisreout = ; frequency to write the running time averaged
and instantaneous distances of all atom pairs involved in restraints
;orire = ; no, yes, orientation restraints
;orire_fc = ; force constant for orientation restraints
;orire_tau = ; time constant for orientation restraints
running average
;orire_fitgrp = ; fit group for orientation restraining, for a
protein backbone is a good choice
;nstorireout = ; frequency to write the running time averaged
and instantaneous orientations
;
; Free Energy
Perturbation--------------------------------------------------------------------------------------------------------------------------------
;free_energy = ; no, yes, Interpolate between topology A to
topology B
;init_lambda = ; starting value for lambda
;delta_lambda = ; increment per time step for lambda
;sc_alpha = ; the soft-core parameter, a value of 0 results
in linear interpolation of the LJ and Coulomb interactions
;sc_power = ; the power for lambda in the soft-core
function, only the values 1 and 2 are supported
;sc_sigma = ; the soft-core sigma for particles which have
a C6 or C12 parameter equal to zero
;
; Non-Eqilibrium
MD---------------------------------------------------------------------------------------------------------------------------------------
;acc_grps = ; groups for constant acceleration
;accelerate = ; acceleration for acc_grps; x, y and z for
each group
;freezegrps = ; Groups that are to be frozen
;freezedim = ; dimensions for which groups in freezegrps
should be frozen
;cos_acceleration = ; the amplitude of the acceleration profile for
calculating the viscosity
;deform = ; The velocities of deformation for the box
elements
;
; Electric
Field------------------------------------------------------------------------------------------------------------------------------------------
;E_x = ; If you want to use an electric field in a
direction, enter 3 numbers after the appropriate E_*, the first number
;E_y = ; the number of cosines, only 1 is implemented
(with frequency 0)so enter 1, the second number: the strength of the
;E_z = ; electric field in V nm-1, the third number:
the phase of the cosine you can enter any number here
;E_xt = ; not implemented yet
;E_yt = ; not implemented yet
;E_zt = ; not implemented yet
;
; Mixed Quantum/Classical Molecular
Dynamics--------------------------------------------------------------------------------------------------------------
;QMMM = ; no, yes, Do a QM/MM simulation
;QMMM-grps = ; groups to be descibed at the QM level
;QMMMscheme = ; normal, ONIOM
;QMmethod = ; Method used to compute the energy and
gradients on the QM atoms
;QMbasis = ; Basisset used to expand the electronic
wavefuntion
;QMcharge = ; The total charge in e of the QMMM-grps
;QMmult = ; The multiplicity of the QMMM-grps
;CASorbitals = ; The number of orbitals to be included in the
active space when doing a CASSCF computation
;CASelectrons = ; The number of electrons to be included in the
active space when doing a CASSCF computation
;SH = ; no, yes, Do a QM/MM MD simulation on the
excited state-potential energy surface
#include "ffgmx.itp"
#include "OneEthane.itp"
[ system ]
;Name
pure ethane
[ molecules ]
;Compound #mols
ethane 32768
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