[gmx-users] Peptide interactions with membrane lipids

[David]

On Sat, 2003-10-11 at 20:07, Aswin Sai Narain wrote:
> Hi all,
>  
> I am trying to simulate the interactions amyloid beta peptide with
> DPPC. I used an mdp file with:
>  
> constrain algorithm: shake
>  
> rvdw=1.0
> rcoulomb=1.8
>  
> Berendsen Temperature coupling was used - 300 k, tau_t=0.1
> Pressure = 1bar, tau_p=1.0
>  
> When i tried running the md i got an error that said:
>  
> 1-4 interactions greater than 1
>  
> Then the simulation stopped completely.
>  
> Can anyone help me with this?
most likely your starting structure is strained, e.g. because of
overlapping water and peptide or lipids and peptide. Do a more thorough
energy minimization and position restrained MD
>  
> Thanks
>  
> Aswin
>  
>  
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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