> On Jun 22, 2015, at 5:10 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,
Kenneth and Dan made good points. I'll just point out here that 12 A is a very big cutoff. This can drastically increase the cost of the simulation. If you reduce this to 8 A, you will likely see a significant increase in performance without degrading your results (since all that does for electrostatic interactions is push more work into reciprocal space).
HTH,
Jason
> 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/
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 22 2015 - 17:30:02 PDT
