Hello Amber Users,
I am performing MD runs through Sander in
Amber 6.0. Everything seems to be working
well, except for the pressure and resulting density
of the PBC simulation. I have set pres0 = 1.0,
and yet the density will steadily decrease from
0.7 (pre-MD density) to 0.4 within 25 ps. I must
therefore assume that the repulsive vdW and electro-
static forces are too high relative to the attractive
forces to produce a density of 1 at 1 bar of pressure.
Any tips (such as altering the compressibility or PME
variables) to obtain a normal density would be appre-
ciated. My input is included for reference and thanks
in advance.
&cntrl imin = 0, irest = 1, ntx = 7,
nstlim = 100000, nsnb = 20, dt = 0.0001,
temp0 = 300, tautp = 0.5, vlimit = 80,
ntt = 1, npscal = 1, ntb = 2, ntp = 1, taup = 1,
ntc = 2, ntf = 2, cut = 10.0, scee = 1.2,
ntwx= 100, ntwe = 100, ntpr = 100,
ntwprt = 0, pres0 = 1.0,
&end
&ewald
nfft1 = 27, nfft2 = 27, nfft3 = 27,
&end
########################
Garrett W Grahek
########################
Dept. of Bioengineering
501 Rhodes Reseach Center
Clemson University
Clemson , SC 29624
voice #864.656.1352
fax #864.656.1822
email: ggrahek_at_clemson.edu
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Received on Tue Jul 11 2000 - 07:54:04 PDT
