Just a thought.
Was lambda=0.0 also minimized itself?
HTH.
Ying-chieh
-----Original Message-----
From: Khabiri, Morteza [mailto:khabiri.med.umich.edu]
Sent: Thursday, August 6, 2015 9:35 AM
To: amber.ambermd.org
Subject: [AMBER] Thermodynamic integration goes wrong in lambda =0 while
lambda = 1 is ok!!
Dear Amber users
I am running thermodynamic integration with amber. I am using the following
input file for running:
TI simulation
&cntrl
imin = 0, nstlim = 150000, irest = 1, ntx = 5, dt = 0.002,
ntt = 3, temp0 = 298.0, gamma_ln = 5.0, ig = -1,
ntc = 2, ntf = 1, ntb = 1,ntp = 0,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1000, ntpr = 100, ntwr = 2000,
icfe = 1, ifsc = 1, clambda = 0, scalpha = 0.5, scbeta = 12.0,
logdvdl = 1,
ifmbar = 1, bar_intervall = 1000, bar_l_min = 0.0, bar_l_max = 1.0,
bar_l_incr = 0.1,
timask1 = ':116,149', timask2 = ':159,160',
scmask1 = ':116,149', scmask2 = ':159,160',
&end
when I am using this input as "lambda=1" the system runs well. But when I
switch to "lambda = 0" the system crashes with the following coordinates:
-2.2263528 0.4948044 1.3902758 -9.8532522 -20.0000000 4.7261966
6.1548176 20.0000000 3.7616364 4.3712168 0.3085792 -0.6998316
11.9788399 -20.0000000 -20.0000000 -20.0000000 20.0000000 20.0000000
3.6102063 2.5685121 -2.9439387 -2.4273888 -20.0000000 -20.0000000
20.0000000 10.4990634 20.0000000 -0.6574321 4.3513134 -1.9494082
15.8827264 -20.0000000 20.0000000 10.8980516 20.0000000 -20.0000000
-0.2922468 3.1186614 -4.0249280 -9.9457371 4.3672343 -20.0000000
12.1206371 -14.9312673 20.0000000 3.3266217 -1.5028986 1.1370716
-20.0000000 -12.9537867 -20.0000000 20.0000000 20.0000000 16.7487781
87.1893599 101.2862751 136.4590540 90.0000000 90.0000000 90.0000000
The system is very well minimized and the minimized system sounds without
problem. Any idea why this happen when the lambda switch to 0?
Thanks
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Received on Wed Aug 05 2015 - 20:30:02 PDT
