On 11/27/13 7:30 PM, Valentina wrote:
I still cannot resolve this problem. Is there any way to find out what is
causing Segmentation Fault? Normally Gromacs provides quite comprehendible
errors, but this one.

I have checked the charges against DFT.

I also have the output of the system simulated with Discover. I am using
that force field (obviously tabulated) and charges used there.

The initial model is taken from Xray and optimised with DFT.

Still md.log terminates with unrealistic T & P on 0th step:

      /      Step           Time         Lambda
               0        0.00000        0.00000

Grid: 4 x 3 x 3 cells
    Energies (kJ/mol)
      Tab. Bonds    Tab. Angles        LJ (SR)   Coulomb (SR)      Potential
     5.44943e+06    4.41001e+11    9.86202e+02   -2.42548e+05    4.41006e+11
     Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
     1.97584e+16    1.97588e+16    1.97588e+16    2.24716e+15    1.99874e+16

BTW - I noticed that I get continuously get a 0 dimension in z direction if
I do energy minimisation with plc = xy - is that right?

My equil.mdp is following - may be some problem there?
I do energy minimisation before equilibration.

/integrator               = md
nsteps                   = 100
dt                       = 0.001
;comm_mode = ANGULAR
nstenergy                = 1
nstxout                  = 1
nstvout                  = 1
energygrps               = System
; cut-offs at 1nm
rlist                    = 0.8
nstlist                  = 10
coulombtype              = user
rcoulomb                 = 0.8
vdw-type                 = user
rvdw                     = 0.8
pbc                      = xyz
periodic_molecules       = yes
; set temperature to 300K
tcoupl                   = V-rescale
tc-grps                  = System
tau-t                    = 1.0
ref-t                    = 500
; and pressure to 1 bar
pcoupl          = no
compressibility  =  4.5e-5
; generate initial velocities
gen-vel                  = no/

I am running with 6-9 LJ, that I provide input to mdrun

I do energy minimisation before equilibration.
em.mdp is
/integrator               = steep
nsteps                   = 500000
emtol                    = 1
emstep                   = 0.001
nstxout                  = 1
nstenergy                = 1
rlist                    = 0.8
pbc                      = xyz
periodic_molecules       = yes
coulombtype              = user
rcoulomb                 = 0.8
vdw-type                 = user
rvdw                     = 0.8
constraints             = none/

I get following output:

/Steepest Descents:
    Tolerance (Fmax)   =  1.00000e+00
    Number of steps    =       500000
Step=    2, Dmax= 5.0e-04 nm, Epot=  4.40635e+11 Fmax= 8.77355e+10, atom=
Step=    4, Dmax= 3.0e-04 nm, Epot=  4.40403e+11 Fmax= 9.61163e+10, atom=
Step=    6, Dmax= 1.8e-04 nm, Epot=  4.40248e+11 Fmax= 1.01812e+11, atom=
Step=    8, Dmax= 1.1e-04 nm, Epot=  4.40181e+11 Fmax= 9.36260e+10, atom= 83
Step=   10, Dmax= 6.5e-05 nm, Epot=  4.40142e+11 Fmax= 9.89456e+10, atom=
Step=   12, Dmax= 3.9e-05 nm, Epot=  4.40115e+11 Fmax= 8.24990e+10, atom=
Step=   14, Dmax= 2.3e-05 nm, Epot=  4.40094e+11 Fmax= 4.88140e+10, atom=
Step=   19, Dmax= 1.7e-06 nm, Epot=  4.40098e+11 Fmax= 4.47573e+10, atom=
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 1 (whichmay not be possible for your system). It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up confout.gro to ./#confout.gro.4#

Steepest Descents converged to machine precision in 20 steps,
but did not reach the requested Fmax < 1.
Potential Energy  =  4.4009390e+11
Maximum force     =  4.8813974e+10 on atom 105
Norm of force     =  5.4008571e+09

I cannot recollect how energy minimisation output should look like - is this

No, this outcome is terrible. Energy should (almost) always be negative and the maximum force should be less than the target Fmax. You have massive forces (10^10 - yikes!) on atom 105, indicating either severe problems with the configuration (which should be obvious upon visual inspection) or, again, your tabulated potential is wrong.

Mark's suggestion before is a good one - simplify the system into its most basic units, down to the level of two atoms and build up to verify your input. From the output shown, the only logical explanations are (1) bad tables or (2) bad configuration.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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