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.yahoo.co.in
===========================================================================
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Received on Fri Apr 01 2005 - 05:53:01 PST
