[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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