[gmx-users] hydrophobicity and forcefileds

[kia balali]

Hello All,

I have a membrame active peptide which I have placed in my equilibrated 
mixed bilayer. I know the possible conformations in which it lies (neutron 
diffraction data...from other members of the lab!). The 1st conformation is 
v. stable, looking at hydrogen bonding with g_hbond. The second conformation

The 2nd conformation is the peptide lying in the same place except flipped 
over so there is a hydrophobic mismatch?
The 2nd one is rather unstable despite me using the same MDP file and more 
or less the same PDB (60 more SPC deleted...ie conflicts). I'm going to look 
at it with G_confirms...to see the differences between starting structure 
and finishing structure.

Can forcefields playa part in this un stability????

I have of course merged my version of lipid.itp & ffgmx2..as recommended by 
Peter Tieleman!

I'll make all this info available online....as soon as I have submitted my 
PhD by the end of the year! Until then sorry if I come across as a bit 
secretive! :-{  Getting a bit paranoid in my late twenties!

Thank you all

Kia



Kia Balali-Mood
Dept. of preclinical Veterinary Sciences
Laboratory of Membrane Biophysics
The Vet School
Faculty group of Medicine & Veterinary Medicine
University of Edinburgh
Summerhall

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