Janne Hirvi wrote:
Hello David!
I read your interesting new article "The Origin of Layer Structure Artifacts in
Simulations of Liquid Water" and I would like to know especially what kind of
NS parameters you have used in the simulations with PME and are the following
parameters correct otherwise?
dt=0.002
nstlist=5
rlist=?
coulombtype=PME
rcoulomb=0.9
vdwtype=cut-off
rvdw=?
I'm attaching my mdp file.
We have just disabled the option to have rlist != rcoulomb with PME.
I am interested especially about the rlist parameter because there seems to be
some energy conservation problems in my water simulations. At least I couldn't
achieve energy conservation with single precision complilation and with
double precision compilation energy is conserved only when switch(shift?)
function is used for vdw interactions (rlist>rvdw>rvdw_switch) and PME for
coulombic interactions (rlist>rcoulomb). If rlist is equal to rcoulomb I need
to update NS list at every time step but with preceding parameters energy is
conserved even when nstlist=10.
So should I use rlist>rcoulomb with PME when nstlist>1 to take into account
movement of atoms/molecules(charge groups) near the real space cut-off limit
(rcoulomb) or is there something I don't understand? Atleast from the manual
someone could get the picture that rlist should be equal to rcoulomb and there
are also different kind of opinions on mailing list?
Maybe Berk can comment?
Thanks for any comments in advance!
Janne
------------------------------------------------------------------------------
Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED]
------------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
;
; File 'mdout.mdp' was generated
; By user: spoel (291)
; On host: matisse
; At date: Sun Aug 11 22:20:40 2002
;
; VARIOUS PREPROCESSING OPTIONS =
title =
cpp = /lib/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0
dt = 0.002
nsteps = 1000000
; 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-temp = 300
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol = 100
emstep = 0.01
; Max number of iterations in relax_shells =
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints =
fcstep = 0
; Frequency of steepest descents steps when doing CG =
nstcgsteep = 1000
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 250
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 or no =
pbc = xyz
; nblist cut-off =
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = PME
rcoulomb-switch = 0
; 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
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = Ener
; 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
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = System
; Time constant (ps) and reference temperature (K) =
tau-t = 0.1
ref-t = 298.15
; Pressure coupling =
Pcoupl = Berendsen
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau-p = 1.0
compressibility = 5e-5
ref-p = 1
; SIMULATED ANNEALING CONTROL =
annealing = no
; Time at which temperature should be zero (ps) =
zero-temp_time = 0
; 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 = shake
; 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
; 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
; 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
rlist = 0.9
rcoulomb = 0.9
rvdw = 0.9
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
