[gmx-users] problem during energy minimization

[chris.neale at utoronto.ca]

1. you're not doing energy minimization as your title suggests, please  
use a better title:
    integrator = md

2. generally, when you have a problem it is useful to try to simplify  
the system (e.g. get rid of those tables) and try to reproduce the  
problem with the simplest system possible before posting.

3. I know that you commented it out, but the following command looks  
like a typo or a misunderstanding... perhaps you meant -DFLEXIBLE ?
    ;define= -DEFLEXIBLE

4. Most relevant to you: This is a little ambitious, don't you think?
    dt = 0.02 ; ps !

Chris.

-- original message --



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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