AMBER: Time step & non-bonded interactions updating

From: Francesco Pietra <>
Date: Sat, 15 Dec 2007 10:39:48 -0800 (PST)

I am having problems of protein stability (in a POPC membrane) during
equilibration and MD although the min heat density equil analyses imitated from
tutorial A3 were OK.

I suspect that the time-step 0.002 (see for example the in file below) is
giving the problems (Minimization was carried out without shake and heating
along the method of tutorial A3)

density equilibration
  imin=0, irest=1, ntx=5,
  nstlim=25000, dt=0.002,
  cut=10, ntb=2, ntp=1, taup=1.0,
  ntc=2, ntf=2,
  ntpr=500, ntwx=500,
  ntt=3, gamma_ln=2.0,
  restraintmask=":77-521 | :POP.O2, P1, O3, O4, O1, C15, C11, N, C12, C13, C14"

Before changing to dt=0.001, may I ask about updating non-bonded interactions,
which might also be relevant. As far as I understand from the manual of Amber9,
updating non-bonded interactions with a *.in file like above occurs by default
to security values. In descriptions from Amber8 non-bonded interactions were
set to be updated every 10 time steps. I would like to have this precise
condition. Much obliged for instructing me how to set that in Amber9.

francesco pietra

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Received on Sun Dec 16 2007 - 06:07:42 PST
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