[gmx-users] problem during energy minimization

[sreelakshmi ramesh]

hai,
              to check if my table is correct i just copied the 6-9 table
for /share/top to local directory ( to check if the prob is same with any
other potential) and grompped it and when i did the mdrun i am still getting
the same error.Any suggestions.

On Fri, May 20, 2011 at 6:29 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>
>>
> --
> ========================================
>
> 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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