Hi,
I received your output files and I note that your problems appear to
start when you start using pmemd.cuda.MPI with 2 nodes
(WTPC_aMD_1-2.out), and that you are running an old version of the
CUDA code (12.1), which is over a year out of date. There have been
major improvements and fixes to the CUDA code since then; the current
version is 12.3.1. Try updating your Amber installation by re-running
configure and re-compiling, then restart the 'WTPC_aMD_1-2.out' run
and see if the temperature jump still occurs.
-Dan
On Mon, Nov 4, 2013 at 12:41 AM, O Z <roza2006.hotmail.fr> wrote:
> Dear Amber users,
>
> I have been running Accelerated MD on my system. I set up my aMD parameters as explained on the Amber manual:
>
> from 10ns MD results (trajectory from 50 to 60 ns).
>
>
>
> ave Dihedral: 2095.80
>
>
> ave EPtot: -194481.05
>
>
> total atoms: 60616
>
>
> protein residues: 199 (3.5*199=696.5)
>
>
> AlphaD: 1/5 * 696.5 = 139.3
>
>
> EthreshD: 696.5 + 2095 = 2791.5
>
>
> alphaP: 60616 * (1/5) = 12123.2
>
>
> EthresP: -194481.05 + 12123.2 = -191091.1
>
> I used these parameters as follow:
>
> &cntrl
>
>
> imin=0,
>
>
> ntx=5,
>
>
>
>
>
> ntpr=25000, ntwx=25000, ntwe=25000, ntwprt=0,
>
>
>
>
>
> ntf=2, ntb=2, cut=12.0, ntp=1, pres0=1.0, comp=44.6, taup=1.0,
>
>
>
>
>
> iwrap=1, nscm=250,
>
>
>
>
>
> nstlim=25000000, dt=0.002,
>
>
>
>
>
> ntt=3, temp0=298.0, tautp=1.0, gamma_ln=3, ig=-1,
>
>
>
>
>
> ntc=2, irest=1,
>
>
>
>
>
> iamd=3,EthreshD=2791.5,
>
>
>
>
>
> alphaD=139.3,EthreshP=-191091.0549,
>
>
>
>
>
> alphaP=12123.2
>
>
>
>
>
> /
>
>
> I am running aMD at 298K but in the output file I noticed
> that the temperature raises a lot from 298K to about 320K (please see file attached).
>
>
> Is that due to the boost function? Or is it a normal behaviour, even if I use the NPT ensemble?
>
> Many thanks for your help.
> Regards.
> OZ
>
> _______________________________________________
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> 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 201
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 Tue Nov 05 2013 - 07:30:03 PST
