Hi again,
I re-did my simulations with the posted .mdp-file. The huge differences
to my formerly posted file are a few vanished semicolons, and after a
fine simulation-run an added dispersion correction due to a pressure
that was slightly higher than expected. Did't really help, made it
worse. But at least the simulations are now at the speed I expected them
to be (gromacs doesen't scale that beautiful under my configuration, any
suggestions???).
Anyhow, two further questions:
First: Is the configuration with r_list = r_vdw and nst_list = 1 a good
choice, especially regarding speed? Suggestions?
(I caught a glimpse at the archives of this forum and couldn't quite
find out why the radius of the neighbour-list has to be smaller than
r_vdw, isn't that list something similar to the verlet-neighbour-lists?
Shouldn't it therefore be bigger? But in this case I'm just curious...)
Second: Am I simulating fixed connections? Are my chosen options on the
.mdp-file therefor correct? Is gromacs doing as less as possible? Got
sometimes at simulations with higher density complains 'bout
constraints. Have I chosen the right configuration in the .itp-file?
to Mark:
Nope, no warnings, posted this time the output-file as well. But I
can't write bigger gro-files (gromacs'complaining something like "can't
allocate memory"). But this isn't a that big problem for me, 125000
molecules are sufficient.
I wanna simulate as fast as possible with only reasonable results, so
I'm unsure why I should use anymore options.
I'm T-coupling at 183K cause I want my bulk at this temperature. No more
reason. And by doing so (along the annealing) I'm simulating a
nucleation-process. Works fine for me.
Considering the missing equilibration: My first posted file missed the
vanished semicolons at the annealing, posted not the most recent file,
my bad, sorry. The simulation-results still were rubbish. And now they
are more or less fine (slightly higher pressure, 5.9 instead of 4.6
bar), of course I'm only measuring at the end of my siimulation run.
Changed the thermostat and r_list, so maybe that was the problem.
Thanks anyway and in advance
Nicolas
Mark wrote:
Nicolas Schmidt wrote:
Hi, I'm doing a comparison in the aspect of speed between gromacs and
an other MD-simulation-program, that isn't providing all the diffrent
options of gromacs.
My problem is, that the results I got from the simulations with
gromacs aren't reasonable. E.g negative pressure and zero kelvin or
ridiculously high pressure and temperature. The simulations are
running more or less fine (though they are too fast ;-) ), but if the
results are rubbish I can't say anything 'bout the speed at all...
I'm assuming your protocol sets up a system of bulk ethane with a
reasonable density, and that there were no warnings you overlooked.
Of course I'm assuming I did a terribly stupid mistake, so I'm asking
you to take a look at my files (added all necessary ones) and correct
me (they are less big than you might emagine, resulting from the
pretty simple molecules I'm buidling up)
Energy minimization before beginning equilibration MD is usually a
good idea. I've no idea why you think turning off basically the entire
set of .mdp options is a good idea, or why you're T-coupling at 183K.
Since you're new, I'd check out
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and
follow along some tutorial material, and then adapt a protocol and
.mdp file to your needs. Trying to measure temperature and pressure
from a single run that didn't have a pre-equilibration phase is just
asking for a crazy result.
Mark
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Gromacs Runs One Microsecond At Cannonball Speeds
2
1ETH ET1 1 0.769 0.769 0.744
1ETH ET2 2 0.769 0.769 0.794
1.53748 1.53748 1.53748
#include "ffgmx.itp"
#include "OneEthane.itp"
[ system ]
;Name
pure ethane
[ molecules ]
;Compound #mols
ethane 64000
NNODES=16, MYRANK=0, HOSTNAME=noco013.nec
NNODES=16, MYRANK=1, HOSTNAME=noco013.nec
NNODES=16, MYRANK=2, HOSTNAME=noco042.nec
NNODES=16, MYRANK=3, HOSTNAME=noco042.nec
NNODES=16, MYRANK=5, HOSTNAME=noco066.nec
NNODES=16, MYRANK=4, HOSTNAME=noco066.nec
NNODES=16, MYRANK=6, HOSTNAME=noco067.nec
NNODES=16, MYRANK=7, HOSTNAME=noco067.nec
NNODES=16, MYRANK=8, HOSTNAME=noco068.nec
NNODES=16, MYRANK=9, HOSTNAME=noco068.nec
NNODES=16, MYRANK=11, HOSTNAME=noco072.nec
NNODES=16, MYRANK=10, HOSTNAME=noco072.nec
NNODES=16, MYRANK=13, HOSTNAME=noco073.nec
NNODES=16, MYRANK=12, HOSTNAME=noco073.nec
NNODES=16, MYRANK=15, HOSTNAME=noco109.nec
NNODES=16, MYRANK=14, HOSTNAME=noco109.nec
NODEID=1 argc=11
NODEID=2 argc=11
NODEID=3 argc=11
NODEID=11 argc=11
NODEID=0 argc=11
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /cacau/rus/itt/ms/bin/mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s ethane_64000.tpr Input Generic run input: tpr tpb tpa xml
-o ethane_64000.trr Output Full precision trajectory: trr trj
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
-c ethane_64000.gro Output Generic structure: gro g96 pdb xml
-e ethane_64000.edr Output Generic energy: edr ene
-g md.log Output Log file
-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-pi pull.ppa Input, Opt. Pull parameters
-po pullout.ppa Output, Opt. Pull parameters
-pd pull.pdo Output, Opt. Pull data output
-pn pull.ndx Input, Opt. Index file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-deffnm string Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-np int 16 Number of nodes, must be the same as used for
grompp
-nt int 1 Number of threads to start on each node
-[no]v bool no Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]sepdvdl bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-[no]multi bool no Do multiple simulations in parallel (only with
-np > 1)
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
NODEID=5 argc=11
NODEID=6 argc=11
NODEID=4 argc=11
NODEID=7 argc=11
NODEID=8 argc=11
NODEID=9 argc=11
NODEID=13 argc=11
NODEID=10 argc=11
NODEID=12 argc=11
NODEID=15 argc=11
NODEID=14 argc=11
Reading file ethane_64000.tpr, VERSION 3.3.1 (single precision)
starting mdrun 'pure ethane'
30000 steps, 99.9 ps.
Writing final coordinates.
M E G A - F L O P S A C C O U N T I N G
Parallel run - timing based on wallclock.
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
NF=No Forces
Computing: M-Number M-Flops % of Flops
-----------------------------------------------------------------------
LJ 24380.617267 804560.369811 27.4
Outer nonbonded loop 3610.504558 36105.045580 1.2
NS-Pairs 66575.323756 1398081.798876 47.6
Reset In Box 3840.128000 34561.152000 1.2
Shift-X 7680.256000 46081.536000 1.6
CG-CoM 3840.128000 111363.712000 3.8
Sum Forces 30721.024000 30721.024000 1.0
Virial 3853.088432 69355.591776 2.4
Update 3840.128000 119043.968000 4.1
Calc-Ekin 3840.256000 103686.912000 3.5
Lincs 1920.192000 115211.520000 3.9
Constraint-V 3840.128000 23040.768000 0.8
Constraint-Vir 1920.192000 46084.608000 1.6
-----------------------------------------------------------------------
Total 2937898.006043 100.0
-----------------------------------------------------------------------
NODE (s) Real (s) (%)
Time: 3124.000 3124.000 100.0
52:04
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 7.804 940.428 2.763 8.686
gcq#2: Thanx for Using GROMACS - Have a Nice Day
Cleaning up all processes ...
done.
;
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 = 1.4 ; 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 = Berendsen ; 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 = ; 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
Gromacs Runs One Microsecond At Cannonball Speeds
2
1ETH ET1 1 0.769 0.769 0.769
1ETH ET2 2 0.769 0.769 0.949
5.53748 5.53748 5.53748
[ 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
editconf -f OneEthane -o ethane_0365 -bt cubic -c -density 10.97555
genbox -cs ethane_0365 -o ethane_0365_64000 -box 61.5
grompp -f md -po out -c ethane_0365_64000 -p ethane_64000 -o ethane_0365_64000
-np 32 -sort -shuffle
(note: 10.97555 g/l ethane are 0.365 mol/l)
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