Hi!
I couldnt spot any wrong settings in your input file (but maybe
somebody else will). This is not normal with nucleic acids. I am
running simulations without this kind of problems.
What you could do is the following:
What happens during equilibration???? Is the T stable????
Try first an NVT equilibration with increasing TEMP0 from 100.0 to 300.0
K gradually (using &wt name list) and then switch to NPT.
For production runs TAUTP and TAUP are too small..try at least 2.0. For
equilibration you can use 0.5 for instance.
Another question is about your input structure. Are you sure that is
correct???
You say your solute is fixed but you have a NTR of 0???? NTR 0 says that
no restraints are applied..............
I also dont understand why cut=9.0 leads to ewald bomb...because I am
always using cut=9.0 and nothing like this happens
Well ...maybe somebody else will be of more help..
Vlad
Thomas Steinbrecher wrote:
>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
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>
--
Vlad Cojocaru
Max Planck Institute for Biophysical Chemistry
Department: 060
Am Fassberg 11, 37077 Goettingen, Germany
tel: ++49-551-201.1327
e-mail: Vlad.Cojocaru.mpi-bpc.mpg.de
home tel: ++49-551-9963204
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Received on Tue Mar 09 2004 - 10:53:00 PST
