Hi,
How long a run takes depends on a lot of factors including how large your
system is, what hardware you are running on, how Amber was compiled, what
simulation options you are using, etc. Before running any production MD you
should benchmark your system (i.e. perform a shorter run to get an idea for
how long your production run is going to take). You can also run
standardized benchmarks and compare to existing benchmarks (typing 'Amber
benchmarks' into Google is a good place to start).
Hope this helps,
-Dan
On Mon, Jun 22, 2015 at 3:10 PM, Morteza Chehel Amirani <
chehelam.ualberta.ca> wrote:
> Hello everyone
>
> I'm wondering how long a typical MD run will be using Amber. It seems
> something is wrong in my relatively short-size model as it takes a long
> time to be simulate for 50 ns. Even if I split the simulations into 10
> stages, it is beyond my expectations. These are the information for my
> simulation:
>
> No. of solute atoms: 160
> No. of water molecules: 2950
> No. of ions: 2
> PBC: Yes
> Total simulation time: 50 ns
> ---------------------------------------
> MD Control parameters:
>
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 12.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 25000000, dt = 0.002,
> ntpr = 25000, ntwx = 25000, ntwr = 100000
> ---------------------------------------
> Job submission command to run in a cluster:
>
> INPUT=md2.in
> OUTPUT=ACNT44_md2.out
> PARM=ACNT44.prmtop
> INPCRD=ACNT44_md1.rst
> RESTART=ACNT44_md2.rst
> MDR=ACNT44_md2.mdcrd
>
> mpiexec -n $CORES pmemd.MPI -O -i $INPUT -o $OUTPUT -p $PARM -c $INPCRD -r
> $RESTART -x $MDR
> ---------------------------------------
>
> Sincerely
> *Morteza Chehel Amirani*
> PhD Candidate
> Department of Mechanical Engineering
> University of Alberta
> 6-29 Mechanical Engineering Building
> Edmonton, Alberta, T6G 2G3
>
> http://www.ualberta.ca/~chehelam/
> _______________________________________________
> 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)
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Received on Mon Jun 22 2015 - 15:00:03 PDT
