[gmx-users] msd not linear and c.o.m removal
Jennifer Williams
Jennifer.Williams at ed.ac.uk
Wed Sep 16 16:19:48 CEST 2009
Hi,
I am running simulations of gaseous molecules (CH4, C2H6, CO2, N2) in
a silica pore (4nm in diameter), cell dimensions, 46 x 44 x 37. This
in an infinite pore in the z direction.
I am interested in looking at diffusion but I am a bit concerned about
the shape of my MSD curves, for a 5ns run, they start off fairly
linear and then at around 2.5ns the slope stops being linear and
levels out - in some cases the gradient goes to zero. So I am getting
a curve rather than a straight line. This is the same whether or not I
use the ?type z option in my command.
At the moment I take the fit the curve between 0.5 - 2.5ns and ignore
the second curvy half of the graph but I'd like to know why this is
happening-Is it because the statistics become poorer for longer runs
or is there something fundamentaly wrong with my system?. Does anyone
know why this is happening?
Another thing I am confused about is whether or not to remove the
centre of mass when one is interested in obtaining the diffusion
coefficient. I have seen on the gromacs forum that linear centre of
mass removal is OK but a colleague has advised me not to remove it
when studying diffusion. What about when applying an acceleration to
obtain transport diffusion coefficients? Is c.o.m removal then needed
or not?
Currently, I am not using any centre of mass removal in my mdrun. Then
I calculate the Ds to be
g_msd ?mol -type z -f traj.xtc -s md.tpr -o msd_z.xvg
D[ CO2] 140.5914 (+/- 75.9583) 1e-5 cm^2/s
However when I include the ?rmcomm command when I run g_msd I get a
very different Ds.
g_msd -rmcomm -type z -mol -f traj.xtc -s md.tpr -o msd_z.xvg
D[ CO2] 0.0118 (+/- 0.0364) 1e-5 cm^2/s
It is difficult to say which value is correct as we don't have
experimental data for comparison.
Has anyone got any advice on this? I have pasted my typical input files below
Much appreciated,
C2H6.itp
[ atomtypes ]
; type mass charge ptype c6 c12
CH3 15.034 0.00 A 0.3512 1.16236218
[ moleculetype ]
; name nrexcl
ET 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CH3 1 ET CH3 1 0.000 15.03452
2 CH3 1 ET CH3 1 0.000 15.03452
[ constraints ]
; ai aj funct c0 c1
1 2 1 0.2353
[ exclusions ]
1 2
2 1
.mdp
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include = -I../top
; e.g.: -DI_Want_Cookies -DMe_Too
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 5000000
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part = 1
init_step = 0
; mode for center of mass motion removal
comm-mode = none
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 1000
nstvout = 1000
nstfout = 1000
; Output frequency for energies to log file and energy file
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file
nstxtcout = 1000
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 = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = yes
; nblist cut-off
rlist = 1.5
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = Shift
; cut-off lengths
rvdw-switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; 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 = yes
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = nose-hoover
; 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 =
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p =
compressibility =
ref-p =
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = no
; Random seed for Andersen thermostat
andersen_seed =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300
gen_seed = 173529
; OPTIONS FOR BONDS
constraints = none
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
continuation = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; 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 =
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps = MCM
freezedim = Y Y Y
cos-acceleration = 0
deform =
.top file
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 1.0 1.0
;
;
[ atomtypes ]
; type mass charge ptype c6 c12
SI 28.08 1.28 A 0.000 0.00
O 15.999 -0.64 A 0.2708 1.538176
OH 15.999 -0.53 A 0.30 1.538176
H 1.008 0.21 A 0.000 0.000
;
; Include forcefield parameters
#include "CH4.itp"
;
;
[ moleculetype ]
; Name nrexcl
MCM 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 SI 1 MCM SI 1 1.2804993 28.086
2 SI 1 MCM SI 2 1.2804993 28.086
3 SI 1 MCM SI 3 1.2804993 28.086
4 SI 1 MCM SI 4 1.2804993 28.086
5 SI 1 MCM SI 5 1.2804993 28.086
??
2139 OH 1 MCM OH 2139 -0.52612471 15.9994
2140 H 1 MCM H 2140 0.20599988 1.00797
2141 OH 1 MCM OH 2141 -0.52612471 15.9994
2142 H 1 MCM H 2142 0.20599988 1.00797
[ bonds ]
; ai aj funct c0 c1 c2 c3
[ constraints ]
; ai aj funct c0 c1 c2 c3
[ angles ]
; ai aj ak funct c0 c1
[ dihedrals ]
; ai aj ak al funct c0 c1
[ system ]
; Name
CH4 in MCM
[ molecules ]
; Compound #mols
MCM 1
CH4 10
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