HM,
It's not clear what your approach is for this simulation. How exactly is your system set up (i.e. system size, number of lipid bilayers, number of waters, number of peptides)? What is the peptide and the mechanism of transport across the membrane? Can you clarify what behavior you expected from this simulation?
In addition, there's already been some work done in our group and our collaborators for lipid parameter sets for Amber. Take a look at the parameter sets Lipid11 and GAFFlipid (Skjevik et al, J. Phys. Chem. B, 2012; Dickson et al, Soft Matter, 2012).
Ben Madej
Walker Molecular Dynamics Lab
On Jan 15, 2013, at 9:18 AM, HM <scienceamber.gmail.com> wrote:
> Hi All,
> In my study, I am trying to see the membrane penetrating behavior of few
> peptides. As a control, I took the peptide which is well known to cross the
> membrane. I prepared the peptide structure (20 amino acid long ) and 20 ns
> simulation to get the stable conformation. Now I prepared the membrane
> (POPC) and kept the peptide over the membrane (using VMD). I generated the
> lipid parameters using AM1-BCC method and then performed the simulation
> (minimization, heating, equilibration.)
>
> Now during simulation the peptide goes away ( within ns) from the lipid
> membrane and it never comes back ( during simulation of 20ns).
>
> I guess there is no point of continuing the simulation ? Can you please
> help me to get rid of this issue.
>
> Thanks,
> HM
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Received on Tue Jan 15 2013 - 10:00:03 PST
