AMBER Archive (2003)

Subject: Re: AMBER: vlimit?

From: Ryan Ye (ryejob_at_yahoo.com)
Date: Tue Dec 23 2003 - 22:04:45 CST

I tried to use gradual warming and a larger value of
taup but it still gave me similar results. This is one
of the md_ntr.in files I tried:
---------------------------------------------------
 &cntrl

  nmropt = 1,
  ntx = 1, irest = 0, ntrx = 1,
ntxo = 1,
  ntpr = 100, ntwx = 5, ntwv = 0,
ntwe = 0,

  ntf = 2, ntb = 2,
  cut = 8.0, nsnb = 10,

  ibelly = 0, ntr = 1,

  imin = 0,
  nstlim = 25000,
  nscm = 0,
  t = 0.0, dt = 0.002,

  temp0 = 300.0, tempi = 100.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  tautp = 0.2,
  vlimit = 15.0,

  ntp = 1, pres0 = 1.0, comp = 44.6,
  taup = 5, npscal = 1,

  ntc = 2, tol = 0.00001

 &end
 &wt
   type='TEMP0', istep1=0, istep2=1500,
                 value1=100.0, value2=300.0,
 &end
 &wt
   type='TEMP0', istep1=1500, istep2=25000,
                 value1=300.0, value2=300.0,
 &end
 &wt
   type='END',
 &end
 &rst
   iat=0,
 &end
Hold the protein fixed
500.0
RES 1 88
END
END
-----------------------------------------------
Could you help me?
Thanks a lot!

--- "David A. Case" <case_at_scripps.edu> wrote:
> On Sun, Dec 21, 2003, Ran Ye wrote:
> >
> > I'm basically following the steps on the "DNA"
> > tutorial
> > to do some MD on proteins. I couldn't get my
> dynamics
> > going because "vlimit exceeded" and "Coordinate
> > resetting (SHAKE) cannot be accomplished". Does
> anyone
> > know how to fix it?
>
> In addition to what Bill Ross suggested, don't try a
> constant pressure
> simulation until you have reached a good temperature
> at constant volume,
> turn down the size of the restraints (from 500 to
> about 5), and use a
> larger value of taup (say 2-5) when you _do_ use
> constant pressure.
>
> ..hope this helps...dac
>
> --
>
>
==================================================================
> David A. Case | e-mail:
> case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax:
> +1-858-784-8896
> The Scripps Research Institute | phone:
> +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
>
> La Jolla CA 92037 USA |
> http://www.scripps.edu/case
>
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>
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