[gmx-users] mdrun-unknown error

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 1 09:09:03 CET 2005

Rahul Karyappa wrote:

> Dear all,
>   I am running MD simulation on my model which consists of polymer, 
> clay and water molecules. I have freezed the clay group in all X Y Z 
> directions. I have inlcuded all the nonbonded interactions in 
> forcefield file. In the clay topology file, as I am freezing the 
> group, I have only included atoms not the bonds, angles and 
> dihedrals. Is it correct or I need to include bonded interactions 
> also? Each unit cell of clay consists of 40 atoms. For every unit cell 
> I have given different charge group nos. Means each charge group 
> consists 40 atoms.
>   When using this topology file I ran the MDrun, it gave me following 
> error:
> Max #atoms in a chargegroup: 40>32
> So I changed the charge group no. in topology file such that now it 
> one charge group contains 20 atoms. Here I also changed the 
> electrostatics interactions to Ewald. Now when I ran MDrun it gave me 
> following error:
> Step0: Segmentation fault
> Where am I doing wrong? please help me out.

Hard to tell, try to minimize first and carefully check energies etc. If 
you don't have bonds you will not have exclusions either so all atoms 
within a molecule will interact. Maybe you need to specify exclusions 

> Thanking you.
> Rahul Karyappa
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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