AMBER Archive (2005)

Subject: Re: AMBER: GB dynamics

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Apr 01 2005 - 15:55:07 CST

I don't know if it would cause the electrostatic problem,
but cold-starting at 300K could disrupt the structure.

BilL

> 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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