400k is very high. Normal water would boil at the pressure you have in the
file. Are you comparing to experiment under this condition? What are the
ionic liquids? How did you obtain there parameters? This sounds like an
advanced research project, so it will be helpful if you already have
extensive experience with more standard simulations.
In principle pmemd will have better speed and comparable accuracy.
On May 22, 2015 5:23 PM, "MOHD HOMAIDUR RAHMAN" <rahmanhpu.gmail.com> wrote:
> 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 Sat May 23 2015 - 03:00:02 PDT
