[gmx-users] problem with energy minimization

[Justin A. Lemkul]

Quoting sanjay23 at iitb.ac.in:

> Dear gromacs user,
> I am doing simulation of Gal1P protein in explicit solvent.when i did
> energy minimization of system i got this warning:-
> Warning: 1-4 interaction between 2779 and 2788 at distance 1.005 which is
> larger than the 1-4 table size 1.000 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.

See here for some general advice:

http://wiki.gromacs.org/index.php/blowing_up

>
> i added table -extention 1.1 in mdp file but i am steel gettingsame
> problem.kindly help me.

This is probably not the best way to handle the problem.  Figure out what the
problem is before allowing your system room to explode.  How did you prepare
the system?  Did you make some sort of model that might have bad atomic
clashes?   What parameters are you using?  Are there any ligands/cofactors that
you've included that might have been given incorrect parameters?

-Justin

> i am pasting em.mdp file for your considerartion
> thanks in advance.
> title               =   Gal1p
> cpp                 =  /lib/cpp
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  50000
> nstlist             =  10
> nstcomm             =  1
> nstxout             =  1000
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.1
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  100
> emstep              =  0.01
>
>
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Justin A. Lemkul
Graduate Research Assistant
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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