From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Jan 18 2012 - 08:12:20 CST
Dear all,
For the past half-year I had a lot of fun building a GPU cluster and
running some ABF MD simulations in a DMPC bilayer. The system simulated is
a spin-labelled peptide composed of alanine either in water or in a DMPC
membrane (Fig1<http://lbf.ijs.si/ajasja/mails/ABF/enhancing-abf-DMPC/Fig1.GIF>
). The colvars (theta and phi) are the polar angles from the C-beta to the
center of mass of the ring of the spin label.
(Fig1<http://lbf.ijs.si/ajasja/mails/ABF/enhancing-abf-DMPC/Fig1.GIF>
).
And in that time I have gathered quite a few ABF related questions:
- *Why is the diffusion along the colvars so much slower in a DMPC
bilayer than in water? *For example compare the colvar trajectories of
Fig2 <http://lbf.ijs.si/ajasja/mails/ABF/enhancing-abf-DMPC/Fig2.GIF>
(water)
and Fig3 <http://lbf.ijs.si/ajasja/mails/ABF/enhancing-abf-DMPC/Fig3.GIF>(DMPC).
If the PMF along the colvars is approx flat, should it still matter
that one system is in DMPC and another in water? So, is the slower
diffusion an intrinsic property of the system or am I perhaps not setting
some ABF parameters correctly?
- *Why are there spikes in the forces applied by ABF in DMPC?* If one
plots the applied forces in water and DMPC the patterns seems quite
different. Larger forces are probably required to move lipid tails so
perhaps this is normal.
Fig3<http://lbf.ijs.si/ajasja/mails/ABF/enhancing-abf-DMPC/Fig3.GIF>
(fa_theta
and fa_phi)
- *Why are there such small energy differences in PMF between water an
DMPC? *(Fig4<http://lbf.ijs.si/ajasja/mails/ABF/enhancing-abf-DMPC/Fig4.GIF>).
If the diffusion along the colvars is slower and more energy is needed to
move lipids out of the way, then this should be seen in the PMF as higher
energy barriers, right? But i'm seeing differences of only 2 kt, which does
not seem that much. I thought this might be due to the fact that I'm
running the simulations above the DMPC transition temperature. So I tried
to lower the temperature (perhaps a bit too much), but at the lower
temperature ABF fails to sample the phase-space very well
(Fig5<http://lbf.ijs.si/ajasja/mails/ABF/enhancing-abf-DMPC/Fig5.GIF>
).
- *How are gradients merged using InputPrefix?* From some quick plots (
Fig6 <http://lbf.ijs.si/ajasja/mails/ABF/enhancing-abf-DMPC/Fig6.GIF>)
the algorithm seems to adjust the offset (how?) and make the
gradient continuous. Overlapping regions are probably averaged over and the
counts of the overlap summed.
- *Is it possible to use Accelerated MD with ABF (and get correct
results)?* This is more of a brainstorming question. Using aMD I could
"soften up" the lipid tails, but this seems very similar to increasing
the temperature, which means I would not know at what temperature and what
phase (liquid ordered, liquid disordered) the lipids are. If indeed this is
even technically possible.
Any insight is appreciated.
Thank you and best regards,
Ajasja Ljubetic,
lbf.ijs.si
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