On 8/2/17 3:23 PM, gangotri dey wrote:
Hello!
I am trying to minimize a periodic MnO2 surface using UFF force fields. I
have previously computed many structures using MnO2 clusters. I did not
face much problem.
However, when I am trying to compute the minimization using the following
minim.mdp there is segmentation error as follows.
; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 5 ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 50; Frequency to update the
neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list
(simple, grid)
coulombtype = PME ; Treatment of long range
electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
(yes/no)
Error:
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps=5
Step=0, Dmax= 1.0e-02 nm, Epot= 3.46301e+34 Fmax= 2.91045e+06, atom=
289
[fen2.hpcc.rutgers.edu:mpi_rank_0][error_sighandler] Caught error:
Segmentation fault (signal 11)
./script: line 5: 54036 Segmentation fault (core dumped) gmx_mpi mdrun
-ntomp 1 -v -deffnm em
I do not understand this problem. Is there anything wrong with my structure
or the minim.mdp?
It's either the coordinates or the force field parameters. You have a
configuration with an energy on the order of 10^34 kJ/mol, which is essentially
infinite, so something is fundamentally flawed.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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