Dear All,
I have run MD simulation of 14 basepairs DNA (in water and nuetralized by
Na+ ions) using protocol as in Amber tutorial. After doing 6 rounds of
minimizations (reducing restrain energy from 25 to 0 kcal/mol.A^2), I ran MD
in NPT ensemble for 100 ps which I obtained canstant box size. Then I
switched to NVE ensemble for 5.6 ns (800 ps for each run). I found that
total energy is not constant, i.e. it increases about 6 kcal/mol (from
-37828 kacl/mol to -37822 kcal/mol) within 5.6 ns. I used Amber 6 on Linux
cluster and input file as below.
Is the obtained total energy normal and acceptable? Is it equilibrium?
#my input file.
------------------------------------------
&cntrl
ntx = 7, irest = 1, nmropt = 0,
imin = 0,
maxcyc = 1000, ncyc = 5000,
ntmin = 1, dx0 = 0.1, dxm = 0.5, drms = 0.0001,
nstlim = 800000,
dt = 0.001, ndfmin = 0, t = 0.0,
timlim = 999999., ntcm = 1, nscm = 2500,
ntpr = 1000, ntwr = 1000,
ntwx = 1000, ntwv = 0, ntwe = 0,
ntwprt = 0, ioutfm = 0, ntrx = 1, ntxo = 1,
cut = 8.0, dielc = 1.0, nsnb = 10,
scnb = 2.0, scee = 1.2, iwrap = 0,
ntb = 1, ntp = 0, npscal = 1,
pres0 = 1.0, comp = 44.6, taup = 2.0,
ntc = 2, tol = 0.000001,
ntf = 2,
ibelly = 0, ntr = 0,
temp0 = 300.0, tempi = 300.0,
ig = 71277, heat = 0.0, tautp = 4.0,
ntt = 0, vlimit = 20.0, dtemp = 1.0,
&end
&ewald
a = 42.0151161, b = 43.0746222, c = 69.8275997,
alpha = 90.000, beta = 90.000, gamma = 90.000,
nfft1 = 45, nfft2 = 45, nfft3 = 72,
order = 4, dsum_tol = 0.00001, eedmeth = 1,
opt_infl = 1, vdwmeth = 1, use_pme = 1,
frc_int = 0, nbflag = 1, skinnb = 1.0
&end
-----------------------------------
Thank you very much in advance.
Hungie
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Received on Fri May 09 2003 - 14:53:02 PDT
