Again here to notice (on extracting the lowest_energy_struct.pdb.#, which was just found in the last (4th) MD run), Amber10 lists WAT until the last ATOM (90375). In contrast, Amber9, used WAT*** after ATOM 9999. Is any change in atom names, I mean particularly those with four characters (which were in Amber9 not conform to the pdb rules, and had to be edited to talk to Chimera, and from it to Amber9).
Thanks
francesco
--- On Sat, 5/24/08, Francesco Pietra <chiendarret.yahoo.com> wrote:
> From: Francesco Pietra <chiendarret.yahoo.com>
> Subject: Fw: Amber9 vs Amber10+MKL benchmark
> To: "Amber" <amber.scripps.edu>
> Date: Saturday, May 24, 2008, 6:51 AM
> Sorry, I forgot to mention that both MD simulations were
> with 8 CPUs, NUMA-type machine.
>
>
> --- On Sat, 5/24/08, Francesco Pietra
> <chiendarret.yahoo.com> wrote:
>
> > From: Francesco Pietra <chiendarret.yahoo.com>
> > Subject: Amber9 vs Amber10+MKL benchmark
> > To: "Amber" <amber.scripps.edu>
> > Date: Saturday, May 24, 2008, 6:48 AM
> > I am comparing two portions of the same classical MD
> > production (pore protein with a large ligand in a POPC
> > hydrated membrane) for Amber9 vs Amber10 on the same
> > hardware. As I found Amber 9 slower by some 5%
> (evaluated
> > from either the "Total time" or the
> "Real
> > time"), I am presenting the situation.
> >
> > The in file reads:
> >
> > prod protein ligand POPC membrane box 80x80
> > &cntrl
> > imin=0, irest=1, ntx=5,
> > nstlim=333334, dt=0.0015,
> > cut=10, ntb=2, ntp=1, taup=2.0,
> > ntc=2, ntf=2,
> > ntpr=1000, ntwx=1000,
> > ntt=3, gamma_ln=2.0,
> > temp0=300.0,
> > /
> >
> >
> > Portion 4: Amber 10 compiled with ifor+MKL 10.1.015,
> > support openmpi-1.2.6 (compiled same Intel).
> >
> >
> > Portion 3: with Amber 9 compiled with ifort 9.1.036,
> > support openmpi-1.2.3 (compiled same Intel).
> >
> > I expected little gain from MKL for classical MD
> because of
> > the overhead, though I was surprised that Amber 10 has
> > suffered so much to turn out to be slower.
> >
> > That the MKL are installed correctly is proved by a
> 40%
> > speed gain by using MKL in a heavy docking simulation
> (were
> > ca 8GB MEM are used).
> >
> > I assume that each nstlim=333334 run of MD should
> require
> > the same time of execution. If this is not wrong, is
> the
> > situation presented amenable to a comment?
> >
> > Thanks
> > francesco pietra
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Received on Sun May 25 2008 - 06:08:12 PDT
