AMBER Archive (2005)

Subject: AMBER: GB dynamics

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Thu Mar 31 2005 - 22:01:30 CST


Dear AMBER users,

I am running an MD simulation of a bulged RNA with
implicit solvent(igb=1).When I neutralized the system
with Na+ ions the electrostatic energy (EELEC) and EGB
is varying too much but all other terms are almost
stable.The EELEC is initially negative (-2652) and
after 22.5 psecs it becomes positive (19) and then
increasing. The EGB is decreasing almost in the same
rate and so the total energy is almost stable. Is it
normal? My .in files are shown below.
=========================================================
minimization run
 &cntrl
  imin = 1,
  maxcyc = 5000,
  ncyc = 2500,
  ntb = 0,
  igb = 1,
  cut = 20
 /
=========================================================
equilibration run
 &cntrl
  imin = 0, ntb = 0,
  igb = 1, ntpr = 100, ntwx = 100,
  ntt = 3, gamma_ln = 1.0,
  tempi = 0.0, temp0 = 300.0,
  nstlim =20000, dt = 0.001,
  cut = 999
 /
========================================================
production run
 &cntrl
  imin = 0, ntb = 0,
  igb = 1, ntpr =100, ntwx = 100,
  ntt = 3, gamma_ln = 1.0,
  tempi = 300.0, temp0 = 300.0,
  nstlim = 200000, dt = 0.001,
  cut = 999
  /
========================================================
Thanks in advance
Mathew

===========================================================================

/\/\athew

Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India

email mathew_kvarghese_at_yahoo.co.in

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