[gmx-users] mdrun running without simulating new steps
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 9 21:27:35 CEST 2009
st wrote:
> Hi,
>
> I now minimized the energy before the mdrun, and still got the same
> problem. I also tried several other things:
> 1. I mdrun the system without water, it runs fine. But once I added
> water, it stops propagating steps/files while still seems running.
> 2. The system has nonzero charge of 0.9, and the Coulomb energy seems
> (very high) the major contribution to the total energy.
> Any suggestion will be appreciated!
>
I would address #2 first. What is the cause of a net charge of 0.9? This
magnitude of charge is non-negligible. What force field are you using? I seem
to recall multiple people having non-zero charges when they used OPLS-AA with
"zwitterion" as the termini (which is wrong for a full protein). Could this be
part of your problem?
-Justin
> below is the output of a recent try:
> ____________________________________________________________________________________________________________________________________________________________________
>
> Input Parameters:
> integrator = md
> nsteps = 40000
> init_step = 0
> ns_type = Grid
> nstlist = 1
> ndelta = 2
> nstcomm = 1
> comm_mode = Linear
> nstlog = 100
> nstxout = 100
> nstvout = 100
> nstfout = 100
> nstenergy = 100
> nstxtcout = 100
> init_t = 0
> delta_t = 0.0005
> xtcprec = 1e+06
> nkx = 50
> nky = 50
> nkz = 80
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = TRUE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = Nose-Hoover
> epc = No
> epctype = Isotropic
> tau_p = 1
> 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 = PME
> 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: 59322
> ref_t: 300
> tau_t: 0.5
> anneal: No
> ann_npoints: 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
> Table routines are used for coulomb: TRUE
> Table routines are used for vdw: FALSE
> Will do PME sum in reciprocal space.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
> A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
>
> Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
> Cut-off's: NS: 1 Coulomb: 1 LJ: 1
> System total charge: -0.900
> Generated table with 4000 data points for Ewald.
> Tabscale = 2000 points/nm
> Generated table with 4000 data points for LJ6.
> Tabscale = 2000 points/nm
> Generated table with 4000 data points for LJ12.
> Tabscale = 2000 points/nm
>
> Enabling SPC water optimization for 6481 molecules.
>
> Configuring nonbonded kernels...
> Testing ia32 SSE2 support... present.
>
>
> Removing pbc first time
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest
> There are: 19775 Atoms
> Max number of connections per atom is 37
> Total number of connections is 53706
> Max number of graph edges per atom is 4
> Total number of graph edges is 26788
> Initial temperature: 0 K
>
> Started mdrun on node 0 Wed Sep 9 10:52:42 2009
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Grid: 8 x 8 x 12 cells
> Energies (kJ/mol)
> Bond Morse Angle G96Angle Proper Dih.
> 3.89303e+02 1.05091e+01 6.55879e+01 7.38907e+00 1.17177e+03
> Ryckaert-Bell. LJ (SR) Coulomb (SR) Coul. recip. Potential
> -3.77214e+00 2.37518e+01 -2.87848e+05 -2.00200e+04 -3.06203e+05
> Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> 6.24804e+02 -3.05578e+05 -3.05578e+05 2.53350e+00 -8.53815e+03
> ________________________________________________________________________________________________________________________________________________________
>
>
>
> --------------------------------------------------
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Sent: Tuesday, September 01, 2009 4:35 PM
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] mdrun running without simulating new steps
>
>>
>>
>> st wrote:
>>> Hi,
>>> I run a two-molecule system with mdrun_d in a water box (~10000
>>> water molecules.)
>>> The program looks running properly (no errors nor warnnings)
>>> However the program seems stop outputting files (because the output
>>> file size stop increases) after about 5min.
>>> The mdrun_d interface looks normal without any errors, the md.log
>>> contains only two saves:
>>
>> <snip>
>>
>>> Grid: 9 x 9 x 14 cells
>>> Energies (kJ/mol)
>>> Bond Morse Angle G96Angle
>>> Proper Dih.
>>> 3.35232e+05 3.27635e+01 7.09937e+02 1.73811e+01 2.47097e+03
>>> LJ (SR) Coulomb (SR) Coul. recip. Potential
>>> Kinetic En.
>>> 1.48669e+05 -4.50390e+05 -1.89304e+04 1.78117e+04 4.38796e+05
>>> Total Energy Conserved En. Temperature Pressure (bar)
>>> 4.56608e+05 4.56608e+05 1.09892e+03 -5.74950e+04
>>> Step Time Lambda
>>> 100 0.05000 0.00000
>>> Energies (kJ/mol)
>>> Bond Morse Angle G96Angle
>>> Proper Dih.
>>> 3.38536e+05 1.06967e+03 2.21584e+04 4.26526e+01 3.13457e+03
>>> LJ (SR) Coulomb (SR) Coul. recip. Potential
>>> Kinetic En.
>>> 8.73487e+04 -5.64854e+05 -4.48577e+04 -1.57422e+05 3.56524e+05
>>> Total Energy Conserved En. Temperature Pressure (bar)
>>> 1.99102e+05 7.60608e+05 8.92881e+02 7.56563e+04
>>>
>>
>> I'd say the system is exploding. Your temperature is oscillating
>> between 1000 K and 893 K using a Nose-Hoover thermostat, and your
>> potential starts off in excess of 10^4 kJ mol^-1. Did you run any
>> sort of energy minimization or weak-coupling equilibration before this
>> run?
>>
>> It's odd that mdrun wouldn't give some sort of LINCS warning or write
>> out step*.pdb files right beforehand, though.
>>
>> -Justin
>>
>>> **********************
>>> ------------------------------------------------------------------------
>>>
>>>
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>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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