[gmx-users] Peptide interactions with membrane lipids
spoel at xray.bmc.uu.se
Sat Oct 11 20:56:01 CEST 2003
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
> 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
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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