for questions about timing you should really run one of the
standard benchmarks on your system and compare it
to the published timings. In your case, run the myoglobin one.
Guillaume Bollot wrote:
> Dear all Users!
> I would like to perform molecular dynamic on a protein pore (3600
> atoms) in continuum with Amber 8.0.
> My problem is with this system, the simulation seems to be very very
> long (md1: 57 hours for 100ps). Is it normal?
> Amber was compiled on AMD64 under Linux (Gentoo) and my input files are :
>
> --------------------------------------------------
> min1.in:
> &cntrl
> imin=1, maxcyc=1000, ncyc=500,
> drms=0.05, igb=1,
> ntb=0,
> cut=12.0,
> ntpr=100,
> &end
> -------------------------------------------------
> md1.in
> &cntrl
> imin = 0,
> irest = 0,
> ntb = 0,
> cut = 12, igb=1,
> ntr = 1,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 1,
> nstlim = 100000, dt = 0.001,
> ntpr = 100, ntwx = 100, ntwr = 100,
> &end
> Restraint on Pore (1-256)
> 0.5
> RES 1 256
> END
> END
> ---------------------------------------------------
> md2.in:
> &cntrl
> imin = 0,
> irest = 1, ntx=5,
> ntb = 0,
> cut = 12, igb=1,
> ntr = 0,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 1,
> nstlim = 400000, dt = 0.001,
> ntpr = 400, ntwx = 400, ntwr = 400,
> &end
> ------------------------------------------------------
> I would like to know if the simulation time is normal and my
> methodology is correct?
> I performed already the Tutorial 2 to estimate the binding energy and
> my simulation were ok.
> Thanks in advance!!!!
>
>
>
>
>
> BOLLOT Guillaume
> Organic Chemistry Department
> University of Geneva
> 30, quai Ernest-Ansermet
> CH-1211 Geneva 4
> tel. +41-22 379 6155
> e-mail: Guillaume.Bollot.chiorg.unige.ch
>
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Received on Mon Oct 31 2005 - 12:53:00 PST
