[gmx-users] forcefields and hydrophobicity

kia balali kiabalali50 at hotmail.com
Mon Jul 28 14:19:00 CEST 2003

Dear Xavier,

Thanks for the rapid reply.

Hi Kia.

>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
>v. stable, looking at hydrogen bonding with g_hbond. The second
>The 2nd conformation is the peptide lying in the same place except flipped
>over so there is a hydrophobic mismatch ? yes

Is that a question, an affirmation a result from simulation/experiments ?
No sorry ...should've explained more clearly. I have 4 different 
orientations of the peptide.
position 2 is exactly the same except it's flipped over so there is a 
hydrophobic mismatch

The same thing applies to models 3 &4 except they are deeper in the bilayer.

Hydrophobic mismatch is not supposed to happen but to be the trigger
of deformation of the peptide(protein)/membrane interface.
yes, I agree
>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
>at it with G_confirms...to see the differences between starting structure
>and finishing structure.

How do you evaluate the stability of your peptide, system ? If the 60 water
molecules are at the interface between the peptide and the membrane could
be a reason for different comportment of your peptide. Do you use the same
starting points ? I guess not.

No, the 2nd model is started by a hydrophobic mis match..hence had to del 
more SPC

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

You mean could different force fields yield to different results with the
same...yes ought to have worded it better!
system ? The answer is no in theory but yes in practice. The simulations
are never long enought. But the most important is the starting point.

The longest these sims will goto willl prob be 2-3ns ..as we don't have a 
beowulf here and i wanna get my PhD sorted ASAP

I feel , it's important to compare the sims..properties...ie h bonding, 
energy , RMSD of the starting ...final structure at the same timepoint...say 

Can try different starting point : position/orientation of your peptide and
if the simulations converge.

Exactly what i'll be doing......no real need to use the pull code etc.....as 
i am modelling neutron data as opposed to performing an in silica expt!

Thanks for the refs. sure they'll be useful


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