Dear Gmx users,
I am trying to do minimization of my system .i
have no problem wehen i grompp it but when i do the mdrun its giving me
some segmentation error.I had attached the output of grompp and mdrun
below.Any suggestions please.Thanks in advance
*OUTPUT OF GROMPP*
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Ion'
Excluding 2 bonded neighbours molecule type 'SOL'
Analysing residue names:
There are: 2 Ion residues
There are: 875 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 5253.00
Largest charge group radii for Van der Waals: 0.039, 0.039 nm
Largest charge group radii for Coulomb: 0.085, 0.085 nm
This run will generate roughly 7 Mb of data
Back Off! I just backed up em.tpr to ./#em.tpr.2#
*OUTPUT OF MDRUN*
Reading file em.tpr, VERSION 4.5.3 (single precision)
Starting 2 threads
WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the
forces deviate on average -2147483648% from minus the numerical derivative
of the potential
WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the
forces deviate on average -2147483648% from minus the numerical derivative
of the potential
Making 1D domain decomposition 2 x 1 x 1
starting mdrun 'NA SODIUM ION in water'
10000 steps, 200.0 ps.
step 0: Water molecule starting at atom 2553 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
step 0: Water molecule starting at atom 2595 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault
*EM.MDP*
title = nacl
cpp = /usr/bin/cpp ; the c preprocessor
;define= -DEFLEXIBLE
integrator = md
dt = 0.02 ; ps !
nsteps = 10000
nstlist = -1
coulombtype = user
energygrps = Na Cl Sol
energygrp_table = Na Cl
vdwtype= user
ns_type = grid
rlist = 1.4
rcoulomb = 1.0
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
pbc=xyz;
; Energy minimizing stuff
emtol = 1000.0
emstep = 0.01
regards,
sree
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