[gmx-users] Re: gromacs 4.6 GB/SA problem and poor performance

[Changwon Yang]

Input files: conf.gro and mdp files

http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM

cpu-imp-RF-inf.mdp

constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps ! 
nsteps              =  0 
nstlist             =  0  
ns_type             =  grid
rlist               =  0 
coulombtype         =  cut-off
vdwtype             =  cut-off
rcoulomb            =  0 
rvdw                =  0 
pbc                 =  no
epsilon_rf	    =  0
rgbradii            =  0
comm_mode           =  angular

implicit_solvent    = GBSA
gb_algorithm        = OBC
gb_epsilon_solvent  = 78.3
sa_surface_tension  = 2.25936

nstxout             = 0
nstfout             = 0
nstvout             = 0
nstxtcout           = 50
nstlog              = 0
nstcalcenergy       = -1
nstenergy           = 50

tcoupl              = berendsen
tc-grps             = system
tau-t               = 0.1
ref-t               = 300


gromacs 4.6 (icc 11.0, centos 5.8, fftw 3.2.2)

Statistics over 101 steps [ 0.0000 through 0.2000 ps ], 10 data sets
All statistics are over 11 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Angle                       4189.86         --    1094.25    2527.08 
(kJ/mol)
Proper Dih.                 6600.66         --    234.905    471.156 
(kJ/mol)
Improper Dih.               121.598         --    32.7574     64.572 
(kJ/mol)
GB Polarization            -32708.8         --    1979.66   -6416.79 
(kJ/mol)
Nonpolar Sol.               158.323         --    13.0032     42.232 
(kJ/mol)
LJ-14                       2346.66         --    180.767    289.567 
(kJ/mol)
Coulomb-14                  26555.4         --    1091.98   -3000.88 
(kJ/mol)
LJ (SR)                           0         --          0          0 
(kJ/mol)
Coulomb (SR)                      0         --          0          0 
(kJ/mol)
Potential                   7263.71         --    1835.42   -6023.06 
(kJ/mol)

gromacs 4.5.3

Statistics over 101 steps [ 0.0000 through 0.2000 ps ], 10 data sets
All statistics are over 11 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Angle                       1840.12         --    178.343    561.256 
(kJ/mol)
Proper Dih.                    6207         --    101.135    210.593 
(kJ/mol)
Improper Dih.               68.4513         --    11.6214    29.5806 
(kJ/mol)
GB Polarization            -13534.1         --    34.3666    95.8711 
(kJ/mol)
Nonpolar Sol.               143.048         --    1.55868    5.13589 
(kJ/mol)
LJ-14                       2380.44         --    26.9563    24.6177 
(kJ/mol)
Coulomb-14                  29155.5         --    64.9054   -176.267 
(kJ/mol)
LJ (SR)                    -5274.28         --    214.048    650.865 
(kJ/mol)
Coulomb (SR)               -38297.8         --    143.656   -398.004 
(kJ/mol)
Potential                  -17311.7         --    451.581    1003.65 
(kJ/mol)


In gromacs 4.5.3 GB/SA problem

Starting from fully linear peptide and using inf cut-off, I always get the
segmentation fault error.
Using finite cut-off, It works fine. 





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