Hi,
Two things I can think of to try:
1) Set iwrap = 1 in your minimization script as well.
2) Use the NetCDF restart format (ntxo = 2).
Also, if you're getting weird characters in your restart file (that
aren't **** which indicate overflow) it's possible your disk is having
some issues. In that case using a binary format like NetCDF might
help, but it might not. Are you able to run the Amber test cases
successfully?
> 2 - Warning: ieee_inexact is signaling
> PMEMD Terminated Abnormally!
Are there no other error messages (either in STDOUT, STDERR, or your
pmemd output file). Without more information it's difficult to say
what may be going wrong or even if it's Amber-related.
-Dan
On Wed, Aug 12, 2015 at 7:36 AM, Khabiri, Morteza <khabiri.med.umich.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Aug 12 2015 - 08:30:06 PDT
