[gmx-users] Nonrepeatable results for gromacs 4.0.5
Erik Marklund
erikm at xray.bmc.uu.se
Mon Jun 8 15:36:22 CEST 2009
jimkress_58 skrev:
>> If you turn off dlb this should not happen. Please try it and
>> report if you see the same effect without.
>>
>
> No, I do not see the same effect if I turn off dlb. However, I am concerned
> that the magnitude of the differences between runs exceeds the expected,
> normal variability (as defined by the RMS deviations of each run), so I am
> exploring that.
>
> Also, if I turn on nosum, as suggested by mdrun, the run with dlb turned on
> diverges. This is also a cause for concern.
>
No, that's expected. See David's reply below. Nosum is only good for
reducing communication, thus increasing performance.
/Erik
> Jim
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of David van der Spoel
> Sent: Sunday, June 07, 2009 3:20 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Nonrepeatable results for gromacs 4.0.5
>
> Jim Kress wrote:
>
>> I've been doing multiple runs using gromacs v 4.0.5 mdrun and a constant
>> topol.tpr input file. Unfortunately, the results that I get in my md.log
>> differ from run to run.
>>
>
> This is due to dynamic load balancing. Due to fluctuations in the CPU
> usage (e.g. due to operating system) your load will vary on each CPU and
> gromacs will try to balance it. Hence you get numerical differences
> because in a computer (a+b)+c != a+(b+c), and ultimately the
> trajectories will diverge.
>
> If you turn off dlb this should not happen. Please try it and report if
> you see the same effect without.
>
>
>> For example,
>>
>> Run 1
>>
>> Started mdrun on node 0 Fri May 22 22:53:51 2009
>>
>> Step Time Lambda
>> 0 0.00000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 1.95406e+02 1.04746e+02 4.97704e+01 4.13260e+01
>>
> 1.40158e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.60139e+03 -2.64656e+04 -2.20714e+04 4.03780e+03
>>
> -1.80336e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.03142e+02 -8.46977e+02 1.92470e-05
>>
>> DD step 9 load imb.: force 29.9%
>>
>> At step 10 the performance loss due to force load imbalance is 8.6 %
>>
>> NOTE: Turning on dynamic load balancing
>>
>> DD step 99 vol min/aver 0.731 load imb.: force 6.9%
>>
>> Step Time Lambda
>> 100 0.20000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.05310e+02 1.30129e+02 5.63474e+01 1.81814e+01
>>
> 1.44270e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.69491e+03 -2.69624e+04 -2.24148e+04 4.19456e+03
>>
> -1.82203e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.14910e+02 -5.19031e+02 1.76248e-05
>>
>> DD load balancing is limited by minimum cell size in dimension Y
>> DD step 199 vol min/aver 0.766! load imb.: force 10.7%
>>
>> Step Time Lambda
>> 200 0.40000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.20550e+02 1.09068e+02 6.93319e+01 5.32511e+01
>>
> 1.43458e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.78241e+03 -2.70319e+04 -2.23627e+04 4.13455e+03
>>
> -1.82281e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.10405e+02 -5.01205e+02 1.70105e-05
>>
>> DD load balancing is limited by minimum cell size in dimension Y
>> DD step 299 vol min/aver 0.750! load imb.: force 3.3%
>>
>> Step Time Lambda
>> 300 0.60000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.17474e+02 8.65489e+01 5.24995e+01 4.72592e+01
>>
> 1.44419e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 3.17643e+03 -2.72841e+04 -2.22597e+04 3.95024e+03
>>
> -1.83095e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 2.96568e+02 1.40098e+03 1.55861e-05
>>
>> DD step 399 vol min/aver 0.700 load imb.: force 5.9%
>>
>> Step Time Lambda
>> 400 0.80000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.43143e+02 9.93116e+01 7.16796e+01 4.63666e+01
>>
> 1.46722e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.84150e+03 -2.70065e+04 -2.22372e+04 4.05976e+03
>>
> -1.81775e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.04791e+02 2.48551e+02 1.61141e-05
>>
>> DD step 499 vol min/aver 0.678 load imb.: force 6.6%
>>
>> Step Time Lambda
>> 500 1.00000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.19638e+02 8.98359e+01 8.99946e+01 5.16612e+01
>>
> 1.46338e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.80267e+03 -2.68507e+04 -2.21335e+04 4.14195e+03
>>
> -1.79916e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.10961e+02 -1.17210e+02 1.71420e-05
>>
>> DD step 599 vol min/aver 0.678 load imb.: force 6.7%
>>
>> Step Time Lambda
>> 600 1.20000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.32938e+02 1.04322e+02 7.11343e+01 2.16046e+01
>>
> 1.45770e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 3.07425e+03 -2.71320e+04 -2.21700e+04 4.17285e+03
>>
> -1.79972e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.13281e+02 5.60002e+01 1.97532e-05
>>
>> DD step 699 vol min/aver 0.664 load imb.: force 13.1%
>>
>>
>>
> ----------------------------------------------------------------------------
>
>> -------------------------------------
>>
>> Run 2
>>
>> Step 0 is the same, but then the results start to differ more and more:
>>
>> Started mdrun on node 0 Sat Jun 6 14:38:03 2009
>>
>> Step Time Lambda
>> 0 0.00000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 1.95406e+02 1.04746e+02 4.97704e+01 4.13260e+01
>>
> 1.40158e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.60139e+03 -2.64656e+04 -2.20714e+04 4.03780e+03
>>
> -1.80336e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.03142e+02 -8.46977e+02 1.92470e-05
>>
>> DD step 9 load imb.: force 32.9%
>>
>> At step 10 the performance loss due to force load imbalance is 8.8 %
>>
>> NOTE: Turning on dynamic load balancing
>>
>> DD load balancing is limited by minimum cell size in dimension Y
>> DD step 99 vol min/aver 0.711! load imb.: force 13.3%
>>
>> Step Time Lambda
>> 100 0.20000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.05314e+02 1.30130e+02 5.63508e+01 1.81808e+01
>>
> 1.44270e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.69491e+03 -2.69627e+04 -2.24151e+04 4.19468e+03
>>
> -1.82204e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.14919e+02 -5.13520e+02 1.76037e-05
>>
>> DD load balancing is limited by minimum cell size in dimension Y Z
>> DD step 199 vol min/aver 0.760! load imb.: force 12.7%
>>
>> Step Time Lambda
>> 200 0.40000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.20600e+02 1.09011e+02 6.92931e+01 5.32915e+01
>>
> 1.43453e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.78045e+03 -2.70297e+04 -2.23626e+04 4.13378e+03
>>
> -1.82288e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.10348e+02 -5.07193e+02 1.69736e-05
>>
>> DD load balancing is limited by minimum cell size in dimension Y
>> DD step 299 vol min/aver 0.757! load imb.: force 12.1%
>>
>> Step Time Lambda
>> 300 0.60000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.18647e+02 8.76939e+01 5.26630e+01 4.67556e+01
>>
> 1.44438e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 3.15118e+03 -2.72121e+04 -2.22108e+04 3.91294e+03
>>
> -1.82978e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 2.93768e+02 1.36397e+03 1.56756e-05
>>
>> DD load balancing is limited by minimum cell size in dimension Y Z
>> DD step 399 vol min/aver 0.688! load imb.: force 12.6%
>>
>> Step Time Lambda
>> 400 0.80000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.37290e+02 9.91231e+01 6.10010e+01 3.87031e+01
>>
> 1.46621e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.68805e+03 -2.68308e+04 -2.22404e+04 4.05083e+03
>>
> -1.81896e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.04120e+02 -2.55369e+02 1.63518e-05
>>
>> DD load balancing is limited by minimum cell size in dimension Z
>> DD step 499 vol min/aver 0.677! load imb.: force 10.1%
>>
>> Step Time Lambda
>> 500 1.00000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.30361e+02 8.47035e+01 8.84842e+01 4.44614e+01
>>
> 1.44045e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.91452e+03 -2.70665e+04 -2.22635e+04 4.18886e+03
>>
> -1.80746e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.14483e+02 1.47268e+02 1.75008e-05
>>
>> DD load balancing is limited by minimum cell size in dimension Z
>> DD step 599 vol min/aver 0.692! load imb.: force 7.7%
>>
>> Step Time Lambda
>> 600 1.20000 0.00000
>>
>> Energies (kJ/mol)
>> G96Angle Proper Dih. Improper Dih. LJ-14
>>
> Coulomb-14
>
>> 2.19896e+02 9.93832e+01 6.10071e+01 2.95745e+01
>>
> 1.45874e+03
>
>> LJ (SR) Coulomb (SR) Potential Kinetic En. Total
>>
> Energy
>
>> 2.81555e+03 -2.71300e+04 -2.24458e+04 4.17303e+03
>>
> -1.82728e+04
>
>> Temperature Pressure (bar) Cons. rmsd ()
>> 3.13294e+02 -3.05949e+02 1.64990e-05
>>
>> DD load balancing is limited by minimum cell size in dimension Z
>> DD step 699 vol min/aver 0.719! load imb.: force 4.9%
>>
>>
>>
> ----------------------------------------------------------------------------
>
>> --------------------
>>
>> Any ideas why I am seeing this?
>>
>> Here is the initial mdrun printed input info:
>>
>>
>> :-) G R O M A C S (-:
>>
>> Groningen Machine for Chemical Simulation
>>
>> :-) VERSION 4.0.5 (-:
>>
>>
>> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2008, 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.
>>
>> :-) mdrun_mpi (-:
>>
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4:
>> Algorithms for highly efficient, load-balanced, and scalable molecular
>> simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447
>> -------- -------- --- Thank You --- -------- --------
>>
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J.
>>
> C.
>
>> Berendsen
>> GROMACS: Fast, Flexible and Free
>> J. Comp. Chem. 26 (2005) pp. 1701-1719
>> -------- -------- --- Thank You --- -------- --------
>>
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for
>> molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp.
>> 306-317
>> -------- -------- --- Thank You --- -------- --------
>>
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> H. J. C. Berendsen, D. van der Spoel and R. van Drunen
>> GROMACS: A message-passing parallel molecular dynamics implementation
>>
> Comp.
>
>> Phys. Comm. 91 (1995) pp. 43-56
>> -------- -------- --- Thank You --- -------- --------
>>
>> parameters of the run:
>> integrator = md
>> nsteps = 5000000
>> init_step = 0
>> ns_type = Grid
>> nstlist = 10
>> ndelta = 2
>> nstcomm = 1
>> comm_mode = Linear
>> nstlog = 100
>> nstxout = 50
>> nstvout = 0
>> nstfout = 0
>> nstenergy = 100
>> nstxtcout = 0
>> init_t = 0
>> delta_t = 0.002
>> xtcprec = 1000
>> nkx = 0
>> nky = 0
>> nkz = 0
>> pme_order = 4
>> ewald_rtol = 1e-05
>> ewald_geometry = 0
>> epsilon_surface = 0
>> optimize_fft = FALSE
>> ePBC = xyz
>> bPeriodicMols = FALSE
>> bContinuation = FALSE
>> bShakeSOR = FALSE
>> etc = Berendsen
>> epc = No
>> epctype = Isotropic
>> tau_p = 0.5
>> ref_p (3x3):
>> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> compress (3x3):
>> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> refcoord_scaling = No
>> posres_com (3):
>> posres_com[0]= 0.00000e+00
>> posres_com[1]= 0.00000e+00
>> posres_com[2]= 0.00000e+00
>> posres_comB (3):
>> posres_comB[0]= 0.00000e+00
>> posres_comB[1]= 0.00000e+00
>> posres_comB[2]= 0.00000e+00
>> andersen_seed = 815131
>> rlist = 1
>> rtpi = 0.05
>> coulombtype = Cut-off
>> rcoulomb_switch = 0
>> rcoulomb = 1
>> vdwtype = Cut-off
>> rvdw_switch = 0
>> rvdw = 1
>> epsilon_r = 1
>> epsilon_rf = 1
>> tabext = 1
>> implicit_solvent = No
>> gb_algorithm = Still
>> gb_epsilon_solvent = 80
>> nstgbradii = 1
>> rgbradii = 2
>> gb_saltconc = 0
>> gb_obc_alpha = 1
>> gb_obc_beta = 0.8
>> gb_obc_gamma = 4.85
>> sa_surface_tension = 2.092
>> DispCorr = No
>> free_energy = no
>> init_lambda = 0
>> sc_alpha = 0
>> sc_power = 0
>> sc_sigma = 0.3
>> delta_lambda = 0
>> nwall = 0
>> wall_type = 9-3
>> wall_atomtype[0] = -1
>> wall_atomtype[1] = -1
>> wall_density[0] = 0
>> wall_density[1] = 0
>> wall_ewald_zfac = 3
>> pull = no
>> disre = No
>> disre_weighting = Conservative
>> disre_mixed = FALSE
>> dr_fc = 1000
>> dr_tau = 0
>> nstdisreout = 100
>> orires_fc = 0
>> orires_tau = 0
>> nstorireout = 100
>> dihre-fc = 1000
>> em_stepsize = 0.01
>> em_tol = 10
>> niter = 20
>> fc_stepsize = 0
>> nstcgsteep = 1000
>> nbfgscorr = 10
>> ConstAlg = Lincs
>> shake_tol = 0.0001
>> lincs_order = 4
>> lincs_warnangle = 30
>> lincs_iter = 1
>> bd_fric = 0
>> ld_seed = 1993
>> cos_accel = 0
>> deform (3x3):
>> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> userint1 = 0
>> userint2 = 0
>> userint3 = 0
>> userint4 = 0
>> userreal1 = 0
>> userreal2 = 0
>> userreal3 = 0
>> userreal4 = 0
>> grpopts:
>> nrdf: 284.733 2919.27
>> ref_t: 300 300
>> tau_t: 0.1 0.1
>> anneal: No No
>> ann_npoints: 0 0
>> acc: 0 0 0
>> nfreeze: N N N
>> energygrp_flags[ 0]: 0
>> efield-x:
>> n = 0
>> efield-xt:
>> n = 0
>> efield-y:
>> n = 0
>> efield-yt:
>> n = 0
>> efield-z:
>> n = 0
>> efield-zt:
>> n = 0
>> bQMMM = FALSE
>> QMconstraints = 0
>> QMMMscheme = 0
>> scalefactor = 1
>> qm_opts:
>> ngQM = 0
>>
>> Initializing Domain Decomposition on 12 nodes Dynamic load balancing: auto
>> Will sort the charge groups at every domain (re)decomposition Initial
>> maximum inter charge-group distances:
>> two-body bonded interactions: 0.597 nm, LJ-14, atoms 5 18
>> multi-body bonded interactions: 0.597 nm, Proper Dih., atoms 5 18
>>
> Minimum
>
>> cell size due to bonded interactions: 0.657 nm Maximum distance for 5
>> constraints, at 120 deg. angles, all-trans: 0.820 nm Estimated maximum
>> distance required for P-LINCS: 0.820 nm This distance will limit the DD
>>
> cell
>
>> size, you can override this with -rcon Scaling the initial minimum size
>>
> with
>
>> 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 12 cells with a
>> minimum initial size of 1.025 nm The maximum allowed number of cells is: X
>>
> 2
>
>> Y 3 Z 2 Domain decomposition grid 2 x 3 x 2, separate PME nodes 0 Domain
>> decomposition nodeid 0, coordinates 0 0 0
>>
>> Table routines are used for coulomb: FALSE
>> Table routines are used for vdw: FALSE
>> Cut-off's: NS: 1 Coulomb: 1 LJ: 1
>> System total charge: 1.000
>> Generated table with 1000 data points for 1-4 COUL.
>> Tabscale = 500 points/nm
>> Generated table with 1000 data points for 1-4 LJ6.
>> Tabscale = 500 points/nm
>> Generated table with 1000 data points for 1-4 LJ12.
>> Tabscale = 500 points/nm
>>
>> Enabling SPC water optimization for 487 molecules.
>>
>> Configuring nonbonded kernels...
>> Testing x86_64 SSE support... present.
>>
>>
>> Removing pbc first time
>>
>> Initializing Parallel LINear Constraint Solver
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> B. Hess
>> P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J.
>> Chem. Theory Comput. 4 (2008) pp. 116-122
>> -------- -------- --- Thank You --- -------- --------
>>
>> The number of constraints is 144
>> There are inter charge-group constraints, will communicate selected
>> coordinates each lincs iteration
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> S. Miyamoto and P. A. Kollman
>> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
>> Water Models J. Comp. Chem. 13 (1992) pp. 952-962
>> -------- -------- --- Thank You --- -------- --------
>>
>>
>> Linking all bonded interactions to atoms
>>
>> The initial number of communication pulses is: X 1 Y 1 Z 1 The initial
>> domain decomposition cell size is: X 1.21 nm Y 1.05 nm Z 1.11 nm
>>
>> The maximum allowed distance for charge groups involved in interactions
>>
> is:
>
>> non-bonded interactions 1.000 nm
>> two-body bonded interactions (-rdd) 1.000 nm
>> multi-body bonded interactions (-rdd) 1.000 nm
>> atoms separated by up to 5 constraints (-rcon) 1.054 nm
>>
>> When dynamic load balancing gets turned on, these settings will change to:
>> The maximum number of communication pulses is: X 1 Y 2 Z 1 The minimum
>>
> size
>
>> for domain decomposition cells is 0.826 nm The requested allowed shrink of
>> DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition
>> cells is: X 0.82 Y 0.78 Z 0.90 The maximum allowed distance for charge
>> groups involved in interactions is:
>> non-bonded interactions 1.000 nm
>> two-body bonded interactions (-rdd) 1.000 nm
>> multi-body bonded interactions (-rdd) 0.826 nm
>> atoms separated by up to 5 constraints (-rcon) 0.826 nm
>>
>>
>> Making 3D domain decomposition grid 2 x 3 x 2, home cell index 0 0 0
>>
>> Center of mass motion removal mode is Linear We have the following groups
>> for center of mass motion removal:
>> 0: rest
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular
>> dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp.
>> 3684-3690
>> -------- -------- --- Thank You --- -------- --------
>>
>> There are: 1604 Atoms
>> Charge group distribution at step 0: 45 50 45 42 46 41 44 45 41 47 51 47
>> Grid: 4 x 4 x 4 cells
>>
>> Constraining the starting coordinates (step 0)
>>
>> Constraining the coordinates at t0-dt (step 0) RMS relative constraint
>> deviation after constraining: 2.38e-05 Initial temperature: 299.151 K
>>
>> Which is, of course, identical between the runs.
>>
>> Thanks for any comments/ advice.
>>
>> Jim
>>
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>
>
>
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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