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/
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Received on Mon Jun 22 2015 - 14:30:02 PDT
