[gmx-users] error in starting/completing minimization

[Justin A. Lemkul]

On 4/23/12 5:38 PM, Rashek Kazi wrote:
> Dear all,
>
> I am trying to conduct some simple ligand binding studies for a protein system
> solvated in water. After inputting the command:
>
> mdrun -v -deffnm em -nt 1
>
> I get the log shown below, nothing completes after this 0 step. Any help would
> be appreciated.
>
> Back Off! I just backed up em.log to ./#em.log.14#
> Getting Loaded...
> Reading file em.tpr, VERSION 4.5.4 (single precision)
> Loaded with Money
>
>
> Back Off! I just backed up em.trr to ./#em.trr.3#
>
> Back Off! I just backed up em.edr to ./#em.edr.3#
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Warning: 1-4 interaction between 1 and 8 at distance 4.764 which is larger than
> the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,

Please see:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 
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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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