On Mon, Aug 3, 2015 at 1:40 PM, Khabiri, Morteza <khabiri.med.umich.edu>
wrote:
> I am doing thermodynamic integration. As far as I know I have to play with
> ntf and ntc. when I put ntf=1 and ntc = 1, the system runing without error
> and any out put. mdout is
Running without SHAKE (ntc=1) is probably not what you want to do,
especially if you're using TIP-like explicit solvent model. If you don't
get any errors when you run without SHAKE this may indicate your initial
system is poorly equilibrated. Your best bet is to try and run a much
shorter simulation to start (e.g. nstlim = 100) and write output every step
to see what is going on (ntpr=1). Then work your way up from there.
-Dan
> empty.
> my input file is as follow:
> TI simulation
> &cntrl
> imin = 0, nstlim = 100000, irest = 1, ntx = 5, dt = 0.002,
> ntt = 3, temp0 = 298.0, gamma_ln = 5.0, ig = -1,
> ntc = 1, ntf = 1, ntb = 1,ntp = 0,
> ioutfm = 1, iwrap = 1,
> ntwe = 1000, ntwx = 10000, ntpr = 10000, ntwr = 20000,
>
>
> 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
>
>
>
> thanks
>
>
>
>
> ________________________________
> From: Khabiri, Morteza
> Sent: Monday, August 03, 2015 9:21 AM
> To: amber.ambermd.org
> Subject: PMEMD: Warning: ieee_inexact is signaling
>
> Dear amber users,
> I am trying to calculate TI in amber cpu version. I have a problem with
> the following error:
>
> PMEMD Terminated Abnormally!
> Warning: ieee_inexact is signaling
>
> I was using exactly the same system with the same input from "
> http://ambermd.org/tutorials/advanced/tutorial9/#remarks" toturial but I
> have got the same error. I would be happy if you can help me.
>
> Thanks
>
> Morteza
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 03 2015 - 13:30:02 PDT
