Hi Dan,
Sorry for the late reply.
The Amber update did not make any change. I decided to run my simulations without using MPI (pmemd.cuda_SPDP instead of pmemd.cuda_SPDP.MPI), which works the temperature is stable.
Thank you for your help.
All the best
OZ
(Please find below a copy of my script)
#BSUB -o /home/Repeats/RP1/%J.log
#BSUB -e /home/Repeats/RP1/%J.err
#BSUB -R "span[hosts=1]"
#BSUB -W 168:00
#BSUB -J Mut_aMD
#BSUB -m emerald8g
#BSUB -n 4
#BSUB -x
source ~/get_X_GPUs 4
MPI_GLOBMEMSIZE=1000000000
export MPI_GLOBMEMSIZE
module load cuda/4.2.9
module load intel/12.1
module load amber/12.9
mpirun -1sided -lsf -np 4 pmemd.cuda_SPDP -O -o MutPC_aMD_1-1_bis.out -i mdrun_RandSeed.in -p Mut_Wat.parm7 -c MutPC_aMD_1-1.rst -ref MutPC_aMD_1-1.rst -r MutPC_aMD_1-1_bis.rst -x MutPC_aMD_1-1_bis.mdcrd -amd MutPC_aMD_1-1_bis.log
> Date: Tue, 5 Nov 2013 08:19:26 -0700
> From: daniel.r.roe.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Temperature raises abnormally during accelerated MD
>
> 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 CUDA code (12.1), which is over a year out of date.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
> >
> > _______________________________________________
> > 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 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 Wed Nov 13 2013 - 22:30:02 PST
