[AMBER] Irregular ligand positioning in simulations

From: Anasuya Dighe <anasuya.mbu.iisc.ernet.in>
Date: Tue, 15 Dec 2015 12:28:43 +0530 (IST)

Dear Amber Users,

 I am simulating a protein-ligand complex for a total of 100ns. The ligand in
question is a peptide inhibitor, that is lodged in the catalytic cleft of the
protein molecule. Upon completing the production run (spanning 100ns of data),
I noticed some peculiar things happening in the trajectory.
 All of a sudden (at a random point in the simulation), the peptide inhibitor
molecule was seen to be present at one end of the solvent box. It continued to
be simulated there. The protein molecule was simulated at the other end of the
box. Please mind the fact that this sudden behavior was not gradual in any
sense ( i.e. the ligand was NOT exiting the catalytic cleft in a step-by-step
 After a few (5-10) frames, the ligand went back to the cleft and this
fluctuating behavior continued for around 10-12 ns, and after that the ligand
was lodged in the cleft.The simulation otherwise completed after 100ns. Also
please note that this behavior was NOT seen since the beginning of the
simulation. In the beginning, the peptide was in the cleft. IT started all of a
sudden at the 49th ns.

 I am quite puzzled at this picture. Is this an imaging issue?
 I am using the iwrap parameter as iwrap = 1
 The .in file for simulation is as follows :

1ns MD
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0, iwrap = 1,
  cut = 10.0, ntr = 0,
  ntc = 2, ntf = 2, ig = -1,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 500000, dt = 0.002,
  ntpr = 500, ntwx = 1000, ntwr = 100000

Please advice me about the steps to take in order to rectify this.
Will something like this have an effect on the data analysis of the trajectory
(using cpptraj)?
Any special commands that i should use during cpptraj, in order to fix this?

Anasuya Dighe
C/o Prof. Saraswathi Vishveshwara,
Lab No. 4, Molecular Biophysics Unit Annexe,
Indian Institute of Science,
Bangalore - 560012

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Received on Mon Dec 14 2015 - 23:00:03 PST
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