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Dear Amber Users,
I have run MD of DNA 40 mers using standard proceder as in amber tutorial.
In equilibrating step, I set ntb=2, ntp=1, ntt=1 (as I understand, it is NPT
ensemble). The result looks fine. Afterthat I run production, I changed
parameters to ntb=1, ntp=0, ntt=0 (NVE ensemble). The result is
-----------------------------------------------------------
NSTEP= 1 TIME(PS) = 40.002 TEMP(K)= 300.47 PRESS = 0.00
Etot = -69897.7413 EKtot = 14421.6638 EPtot = -84319.4051
BOND = 335.1852 ANGLE = 714.9178 DIHED = 777.8773
1-4 NB= 356.3319 1-4 EEL= -3466.9451 VDWAALS= 9955.2497
EELEC = -92992.0221 EHBOND = 0.0000 CONSTRAINT = 0.0000
Ewald error estimate: 0.6313E-04
-----------------------------------------------------------
I am surprised becuase PRESS is always zero for all NSTEPs. Is it correct?
Moreover, input file is at below.
Any suggestion is appreciated. Many thanks in advance.
Hungie.
***input file***
running production step
&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 = 250000,
dt = 0.002, ndfmin = 0, t = 0.0,
timlim = 999999., ntcm = 1, nscm = 2500,
ntpr = 500, ntwr = 500,
ntwx = 5000, ntwv = 0, ntwe = 0,
ntwprt = 0, ioutfm = 0, ntrx = 1, ntxo = 1,
cut = 9.0, dielc = 1.0, nsnb = 10,
scnb = 2.0, scee = 1.2, iwrap = 1,
ntb = 1, ntp = 0, npscal = 1,
pres0 = 1.0, comp = 44.6, taup = 0.2,
ntc = 2, tol = 0.0005,
ntf = 2,
ibelly = 0, ntr = 0,
temp0 = 300.0, tempi = 100.0,
ig = 71277, heat = 0.0, tautp = 0.2,
ntt = 0, vlimit = 20.0, dtemp = 1.0,
ipol = 0, jfastw = 0,
ivcap = 0, matcap = 0, fcap = 1.5,
&end
&ewald
a = 48.5648288, b = 49.6685218, c = 97.5740020,
alpha = 90.000, beta = 90.000, gamma = 90.000,
nfft1 = 50, nfft2 = 50, nfft3 = 100,
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
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Received on Wed Oct 31 2001 - 05:31:20 PST
