AMBER Archive (2006)

Subject: AMBER: AMBER 8 VS AMBER 7

From: venditti2_at_unisi.it
Date: Thu Mar 02 2006 - 13:54:47 CST

Dear all,
I carried out two simulations on the same RNA molecule using both AMBER 8
and AMBER 7.
I used exactly the same input files, just changing the Temperature control
method.
I run two equilibration steps using the input files pr.in and em.in
(please, see below). Then I slowly heated the sistem at 300K using the
input file md1.in and then I rund 10ns of unrestrained MD.
Surprisengly the minimized structures look very diffent and the
unrestrined MD trajectories show a very different behaviour: I obtained a
very stable trajectory using AMBER 7 and an instable one using AMBER 8.
How may I solve this mistake?
Many thanks in advance,
Vincenzo

1)pr.in
 &cntrl
  imin = 1,
  maxcyc = 1000,
  ncyc = 500,
  ntb = 1,
  ntr = 1,
  cut = 10
 /
Hold the RNA fixed
500.0
RES 1 24
END
END

2)em.in
 &cntrl
  imin = 1,
  maxcyc = 2500,
  ncyc = 1000,
  ntb = 1,
  ntr = 0,
  cut = 10
 /

3)md1.in
 &cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 1, (I used ntt = 3 in AMBER 8)
  tautp = 0.2, (I used gamma_ln = 1.0 in AMBER 8)
  nstlim = 10000,
  dt = 0.002,
  ntpr = 500,
  ntwx = 500,
  ntwr = 1000
 /
Keep RNA fixed with weak restraints
10.0
RES 1 24
END
END

4)md2.in
 &cntrl
  imin = 0,
  irest = 1,
  ntx = 7,
  ntb = 2,
  pres0 = 1.0,
  ntp = 1,
  taup = 2.0,
  cut = 10,
  ntr = 0,
  ntc = 2,
  ntf = 2,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 1, (I used ntt = 3 in AMBER 8)
  tautp = 0.2, (I used gamma_ln = 1.0 in AMBER 8)
  nstlim = 5000000,
  dt = 0.002,
  ntpr = 500,
  ntwx = 500,
  ntwr = 1000
 /

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