[gmx-users] how to build up fixed connections? how to simulate no electrostatics?

Nicolas Schmidt nicolas-schmidt at gmx.de
Mon Aug 13 17:52:40 CEST 2007


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
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; 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
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