Accelerated MD with transmembrane protein

From: Kevin Kastner (
Date: Thu Apr 10 2014 - 13:40:26 CDT

  Hello all! I am trying to use accelerated molecular dynamics on NAMD for
a protein that is inside of a lipid bilayer and am having trouble.
Previously, I had set up and run the simulation using the NAMD membrane
tutorial and have gotten that to work (though I have converted it to use
the amber force field instead of CHARMM). From other sources I have
calculated the energies and alphas for each of the protein + system and the
membrane to be the following:

accelMDE = <dihedral energy from standard simulation> + 4 * (# of residues)
+ 40 * (# of POPC molecules)
accelMDalpha = 1/5 * 4 * (# of residues) + 20 * (# of POPC molecules)
accelMDTE = <total energy from standard simulation> - <dihedral energy from
standard simulation> + 0.16 * (# of total atoms)
accelMDTalpha = 0.16 * (# of total atoms)

  I have tried running with these new parameters both starting after the
three preparation steps that need to be done with transmembrane systems
(melting the lipid tails, then constraining the protein, and finally
letting the whole system equilibrate) and also starting at the very
beginning with the three steps using aMD, but the system crashes after a
short while every time. Usually the error has to do with the SHAKE or
RATTLE algorithms.
  Does anyone know anything else I need to do to get this to work? Do I
need to reduce the size of the timesteps from 2fs to 1fs? Or do I need to
do something else? Oh, I do not know if this makes a difference, but I am
also trying to run this on GPUs, rather than CPUs. Is aMD not compatible
with GPU-accelerated MD? I would appreciate any help that anyone can
provide. Thank you!

 - Kevin Kastner
"For me, insanity is super sanity. The normal is psychotic. Normal means
lack of imagination, lack of creativity." - Jean Dubuffet

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