Hello gmx users,
My system for NVT equilbration runs into segmentation fault as soon as
I try to run it.
It does not give any warning or hint of what might be going wrong.
Since I am a new user I am having difficulty exploring the plausible
reasons.
System: Protein( polyhistidine), 20 2,5-dihydroxybenzoic acid anions,
1:1 water: methanol (~3000 molecules of each) in 8 nm cube
I had had EM of the system using steepest decent. Outcome:
Steepest Descents converged to machine precision in 15 steps, but did
not reach the requested Fmax < 1000.
Potential Energy = 1.5354981e+19
Maximum force = inf on atom 651
Norm of force = inf
So that's broken already - you have enormous positive energy and
infinite forces. Stop there and fix it. Either your starting
configuration has severe atomic overlaps (go and visualize it with the
periodic box), or some of your topology is broken (try a box of methanol
on its own, try the protein in vacuum, try a single acid in vacuum)
Mark
*The minim.mdp *is:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep = 0.02 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long
range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
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)
constraints = none
*The nvt.mdp*:
title = hist NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = none ;
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
I tried to decrease the step size, that also runs into seg fault error.
Kindly guide.
Thanks,
SN
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
