[gmx-users] problem during energy minimization

[Justin A. Lemkul]

sreelakshmi ramesh wrote:
> 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
> 

These messages indicate that your tables are severely malformed.  I suspect your 
system is collapsing from an unrealistic physical model.

-Justin

> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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