[AMBER] Suggestions on crossing energy barrier to break strong HBs

From: Amit Sharma (Asstt. Prof., MCARS) <"Amit>
Date: Sat, 30 Jan 2021 05:10:35 +0530

Hi,

I am simulating a protein system in which a heme molecule is strongly
hydrogen bonded (via 2 HB's) to one of the protein residues. These HB's are
expected to break during the course (around ~700 ns) of NPT run and shall
lead to the further cascade of bond breaking/making in the protein.

But, I do not see this initial breaking of HB's in my simulation. The run
parameters I am using are as follows

  imin = 0, irest = 1, ntx = 7, ntb = 2,
  pres0 = 1.0, ntp = 1, taup = 0.5, gamma_ln = 1.0,
  cut = 8.0, ntr = 0, ntc = 2, ntf = 2,
  tempi = 298.0, temp0 = 298.0, ntt = 3

May I please get some suggestions about what changes can be tried in the
simulation, so that the system could cross the energy barrier needed to
initiate the breaking of these HBs between protein residue and heme
molecule.

Thank You,

Amit




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Received on Fri Jan 29 2021 - 16:00:02 PST