Re: [AMBER] Heating up the sytem

From: Senthil Natesan <sen.natesan.yahoo.com>
Date: Sat, 4 Sep 2010 07:57:10 -0700 (PDT)

Hi Hirdesh,

Why don't you consider changing temp0 = 100.0 for first 10ps
and then switch to ntb=2 (constant pressure) and increase your
temp0 to 300 for another 20 ps.

I had problem in equilibrating the solvent around protein-ligand complex and
the following runs fixed the problem (Thanks to Dr. Ross Walker)
you can try the following template for parameters.

run # 1
&cntrl
  imin = 0,
  ntpr = 100,ntwx = 100, ntwr = 1000,
  nstlim = 10000,dt = 0.001,
  tempi = 0.0, temp0 = 100.0,
  ntb = 1,
  ntr = 1,
  cut = 8.0,
  ntt = 3, gamma_ln = 1.0
  /
Hold the protein fixed
10.0
RES 1 122
END
END

run # 2

&cntrl
  imin = 0,irest=1, ntx=7,
  ntb=2, pres0=1.0, ntp=1,
  taup=2.0,
  ntpr = 100,ntwx = 100, ntwr = 1000,
  nstlim = 20000,dt = 0.001,
  tempi =100.0, temp0 = 300.0,
  ntr = 1,
  cut = 8.0,
  ntt = 3, gamma_ln = 1.0
  /
Hold the protein fixed
10.0
RES 1 122
END
END

Good luck,

Senthil




________________________________
From: hirdesh kumar <hirdeshs8.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Fri, September 3, 2010 4:51:49 AM
Subject: [AMBER] Heating up the sytem

Hi All,
I want to heat my system slowly to prevent artifacts generation. I run the
below mentioned script for initial heating equilibration. But still the
system got heated up very quickly and within 3ps interval the temprature
reaches to 276 K. i need help regarding heating the system slowly.

&cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10.0,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 1.0,
  nrespa=2,
  nstlim = 100000, dt = 0.002,
  ntpr = 100, ntwx = 100, ntwr = 1000,
/
Keep Protein fixed with weak restraints
10.0
RES 1 122
END
END

--
Hirdesh
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Received on Sat Sep 04 2010 - 08:00:04 PDT
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