Equilibrium much more complex than just minimization. Ours tend to be about
10 different steps. GB simulations are particularly sensitive to careful
equilibration. Also I would not suggest igb=1. This is an old model with
well documented serious weaknesses. For proteins you should use igb=8. See
that paper (Nguyen et al JCTC 2013) for more details, as well as
equilibration examples. Also see the Nguyen et al JACS 2014 for examples of
proteins in GB.
On Apr 16, 2016 12:20 PM, "Avik Bhattacharjee" <avik8394.gmail.com> wrote:
> Hi, Dan,
> Thanks for your reply. But I have already done a long minimization run
> prior to the production( of 250000 steps), and from the output file of the
> minimization run it is clearly visible that the energy is becoming constant
> for the minimization. But still I am facing this problem. And regarding the
> cut off I was just following the tutorial for simulation of a DNA fragment
> in implicit solvent, that is why I have choose 12 angstrom distance. Still
> I will try with the keyword "cut=999.0".
> Regards,
> Avik
>
> On Sat, Apr 16, 2016 at 10:20 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > 'vlimit' errors are usually indicative of improper prior
> > equilibration. You may need more minimization prior to your production
> > run. Also, a cutoff of 12 Angstroms is far too small to be considered
> > reliable for a GB simulation. You should really run with an
> > effectively infinite cutoff (9999.0 is usually adequate), otherwise
> > you are omitting a lot of important interactions from your system.
> >
> > -Dan
> >
> > On Sat, Apr 16, 2016 at 10:43 AM, Avik Bhattacharjee <avik8394.gmail.com
> >
> > wrote:
> > > Hi,
> > > I was trying to simulate a protein in implicit solvent environment. i
> > have
> > > first minimized the structure and then tried to carry out a production
> MD
> > > in implicit solvent using the following input parameters:
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > *hca MD Generalised Born, 12 angstrom cut off &cntrl imin = 0, ntb =
> 0,
> > > igb = 1, ntpr = 500, ntwx = 500, ntt = 3, gamma_ln = 1.0, tempi =
> > 300.0,
> > > temp0 = 300.0, nstlim = 100000, dt = 0.002, cut = 12.0 /*
> > >
> > > but as soon as I start the simulation the structure started to
> collapse.
> > > Here I am annexing a copy of the output file:
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > *vlimit exceeded for step 496; vmax = **********vlimit exceeded for
> > > step 497; vmax = **********vlimit exceeded for step 498; vmax =
> > > **********vlimit exceeded for step 499; vmax = ********** NSTEP =
> > > 500 TIME(PS) = 1.000 TEMP(K) =********* PRESS = 0.0 Etot
> > > = NaN EKtot = 19874662.4076 EPtot =
> > > NaN BOND = 852405.4613 ANGLE = 94829.9606 DIHED =
> > > 8798.7961 1-4 NB = 71329408.5341 1-4 EEL = 11302.8746 VDWAALS
> =
> > > ************** EELEC = -18466.3455 EGB = NaN
> > > RESTRAINT =
> > > 0.0000
> >
> ------------------------------------------------------------------------------vlimit
> > > exceeded for step 500; vmax = **********vlimit exceeded for step
> > 501;
> > > vmax = **********vlimit exceeded for step 502; vmax =
> **********vlimit
> > > exceeded for step 503; vmax = **********vlimit exceeded for step
> > 504;
> > > vmax = **********vlimit exceeded for step 505; vmax =
> **********vlimit
> > > exceeded for step 506; vmax = **********vlimit exceeded for step
> > 507;
> > > vmax = **********vlimit exceeded for step 508; vmax =
> **********vlimit
> > > exceeded for step 509; vmax = ***********
> > > Please help me out
> > > *.*
> > >
> > > With regards,
> > > Avik Bhattacharjee
> > > IIT KGP
> > > INDIA*.*
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sat Apr 16 2016 - 11:00:03 PDT
