[AMBER] Regarding high temp simulation of DNA and amber MD module

From: MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
Date: Sat, 23 May 2015 02:53:29 +0530

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

Input for MD simulation
  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,

Thanks in advance for your valuable suggestion
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Received on Fri May 22 2015 - 14:30:02 PDT
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