Dear Amber users
I am currently using amber TI facility to calculate the energy. I am using amber 14 with cpu. After runing minimization and also few picoseconds (more than 100ps), the calculation face with several problems:
1- the output restart file will be either empty or it will have the wierd lines:
^.^.^.^.^.^.^.^.^.^.^.^.^.^.^.^.^.^.^.^.^.^
40.1663439 36.6236899 75.9709807 40.7386045 37.6774349 75.0150665
58.5171197 14.8292466 98.3307534 57.8452195 14.9685980 97.6472285
59.2496662 14.4827046 97.7935788 27.7160385 17.6966860 12.6175659
26.7565847 17.8057902 12.4188381 28.0899501 17.6401140 11.7086371
43.4132517 79.1267615 39.4152244 43.7105433 78.6583376 38.5828976
44.0489276 79.9008110 39.4693903 81.6629577 72.6072258 98.5898773
first I thought it maybe is the minimization problem, but I have minimized my system by increasing the cycle number but still I face with problem after some time.
I have also decreased the time step to 0.001 but it did not work.
the minimization input is:
minimisation
&cntrl
imin = 1, ntmin = 2, maxcyc = 1000,
ntpr = 20, ntwe = 10,
dx0 = 1.0D-7,
ntb = 1,
icfe = 1, ifsc = 1, clambda = 1, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':124,141', timask2 = ':159,160',
scmask1 = ':124,141', scmask2 = ':159,160',
!method 2:
!scmask1 = '', scmask2 = ':163.HG=',
/
&ewald
/
and the runing input is:
TI simulation
&cntrl
imin = 0, nstlim = 9375, irest = 0, ntx = 1, dt = 0.001,
ntt = 3, temp0 = 298.0, tempi = 200, tautp = 1.0, ig = -1,
ntc = 2, ntf = 1, ntb = 1,ntp = 0,
ioutfm = 1, iwrap = 1,
ntwe = 100, ntwx = 100, ntpr = 100, ntwr = 100,
icfe = 1, ifsc = 1, clambda = 1, 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 = ':124', timask2 = ':159',
scmask1 = ':124', scmask2 = ':159',
&end
and 2nd error:
2 - Warning: ieee_inexact is signaling
PMEMD Terminated Abnormally!
I have several systems which are running with TI with the same method and input file. Some of them running well but some faced this problem.
Any idea what cause this problem.
Thanks
Morteza
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Received on Wed Aug 12 2015 - 07:00:05 PDT
