Dear AMBER users,
I am trying to simulate a DNA decamer in explicit solvent
using periodic boundary conditions with neutralizing Na+
ions, similar to the simulations described in Srinivasan et
al. ACS 1998.
I loosely followed the equilibration procedure detailed in
the first tutorial on the AMBER homepage (details see
below), but I run into trouble:
After equilibration, my production runs yielded system
temperatures of ~360K. I used tautp=1.0 and temp0=300 as
parameters. Changing tautp to 0.5 or temp0 to 270 let the
temperature level off at ~330K. Can someone tell me if this
behaviour is to be expected? I was wondering if something
in my equilibration procedure is wrong or if this is a
known problem in DNA simulations. Is further lowering the
target temperature temp0 a valid workaround if it results
in a system temperature of ~300K or will this cause a more
unnatural trajectory?
Many thanks in advance for any help and comments,
kind regards,
Thomas
Details of my equilibration procedure:
I do an initial minimization, followed by 25ps of constant
pressure equilibration with restrained solute (yields a
density of ~1) and subsequent minimization without
restraints. I then equilibrate my system for 50-400 ps at
constant volume conditions to equilibrate the system
temperature (longer runs don't seem to change the resulting
temperature in the production runs), followed by 25 ps of
constant pressure simulation to equilibrate density. I use
time constants of 0.2 ps for tautp and taup during
equilibration. I use cut=12.0, because cut=9.0 leaded to
EWALD bomb failures.
My mdin file for production runs
&cntrl
imin = 0, nmropt = 0, ntx = 5, irest = 1,
ntrx = 1, ntxo = 1, ntpr = 5000, ntave = 0,
ntwr = 5000, iwrap = 0,
ntwx = 5000, ntwv = 0, ntwe = 0, ioutfm = 0,
ntwprt = 0, idecomp = 0,
ntf = 2, ntb = 2, dielc = 1, cut = 12.0,
scnb = 2.0, scee = 1.2, nsnb = 10, ipol = 0,
ibelly = 0, ntr = 0,
nstlim = 500000, nscm = 1000, t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 100, ig = 72352,
heat = 0.0, ntt = 1, vrand = 0, tautp =
1.0,
vlimit = 20.0,
ntc = 2, tol = 0.00001,
ntp = 1, pres0 = 1.0, comp = 44.6, taup = 1.0,
npscal = 1,
&end
If anybody is interested, I will of course send my other
input and output files.
Thomas Steinbrecher
Institut für physikalische Chemie
Albertstr. 23a
79108 Freiburg
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Mar 09 2004 - 10:53:00 PST
