From: Haleh a (halehabdi_at_sabanciuniv.edu)
Date: Thu Mar 17 2016 - 11:39:45 CDT
Dear NAMD user's,
I am applying ABF for a conformational change between two states of a
protein. The overall RMSD is 3.15 and I use RMSD colvar to calculate the
PMF value for such a conformational change. I keep the wall constant,
Number of samples, rmsd and atom groups constant while changing only the
simulation time. The whole conformational change under ABF takes place in 1
ns. However, I observe different PMF values if I prolong the simulation. I
repeated the simulation for 1, 2,3,4,5,10,15 and 20 ns long simulations and
for each case I get PMF values within 508-660 kcal/mol where the smallest
PMF value does not correspond to the shortest simulation. My question is
why am I getting such a different PMF values for different simulation
lengths? And how can I optimize the simulation time? If the full
conformational change is achieved within 1 ns, is that much time enough for
ABF application ?
Many thanks,
Haleh Abdizadeh
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