Dear Amber users
I am trying to simulate DNA in ionic liquids at high temperature. Due to
presence of ionic liquids in simulation box, this box have very large no of
cation and anion. So electrostatic and Vander waals energy will play a
major role in dynamics behavior of system.
So my concern is about amber simulation module. Earlier in my lab, we are
following a protocol that is based on sander.mpi module of AMBER. Now I am
planning to run fresh all system on pmemd.mpi or pmemd.cuda.mpi. So how my
result will affect due to shifting from sander.mpi to pmemd.mpi or
pmemd.cuda.mpi. (In term of non-bonded interaction). Which module is
optimal in case accuracy and speed. I am using full ewald method for
calculating electrostatic interaction with cutoff 15.0.
Also at 400K MD simulation, what are those parameters that I have to look
carefully.
Input for MD simulation
NPT.400K,
&cntrl
imin = 0, ntx = 7, irest = 1,
ntpr = 1000, ntwx = 1000, ntwe = 0,
ntc = 2, ntf = 2,iwrap=1, cut=15.0,
nstlim = 2500000, dt =0.002, ioutfm=1,
tempi=400.0, temp0 = 400.0, ntt =1, tautp =0.5,
ntb = 2, ntp = 1, taup = 0.5, pres0 =1.0,
&end
&ewald
EW_TYPE=1
&end
Thanks in advance for your valuable suggestion
Regards
Rahman
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Received on Fri May 22 2015 - 14:30:02 PDT
