[gmx-users] About EM Error (simulation exploding)

[Justin Lemkul]

On 7/30/12 1:07 PM, vidhya sankar wrote:
> Dear Justin, Thank you for your Previous Reply.
>                       I have got the following Error in EM using steepest Descent method in   gromacs
>
> Warning: 1-4 interaction between 4728 and 4733 at distance 3.030 which is larger than the 1-4 table size 3.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>

If energy minimization fails, then there is something unphysical about the 
starting geometry that cannot be resolved.  Note that 3.0 nm is a very long 
distance for a normal 1-4 interactions.  What are these atoms and why are they 
linked by 3 bonds?

> I know That my System  is exploding .I have checked that my ouput .gro file in VMD there is No error . in my system. Then What KInd of Physical Parameter  lead to  error
> My box size is
>
> ./editconf_d -f 1OG2O.gro   -o 1OG2Onewbox1.gro    -center 7.0 8.0 7.0  -box 14.0 16.0 14.0
>
> my Em.mdp file as follows
> integrator  = steep
> emtol       = 1000
> emstep      = 0.01
> constraints = none
> nsteps      = 50000
> nstlist     = 1
> ns_type     = grid
> rlist       = 2.0
> coulombtype = PME
> rcoulomb    = 2.0
> rvdw        = 2.0
> pbc         = xyz
>
>

The cutoff values seem arbitrary.  There is no force field in Gromacs that uses 
2.0 nm for short-range nonbonded cutoffs.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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