On Mon, Mar 28, 2011 at 1:00 PM, Hashem Taha <htahaphd.gmail.com> wrote:
> Thanks for the suggestions, but I am still obtaining the same outcome. yes,
> PTR is a phosphorylated Tyrosine residue. I have also attempted larger
> timesteps (0.001 and 0.002), but with no luck. For my initial heating
> protocol, I did use what you suggest. However, once I started having these
> problems, I modified my input file to include more gradual heating (hence
> the many &wt statements). I also visualized what is happening throughout
> the
> heating process, but there was no indication of a hydrogen atom collapsing
> into another.
>
> side note: If it were the case, how would you treat/workaround the
> situation
> with hydrogen collapse in the presence of phosphate groups?
>
Give it a small repulsive VDW radius to prevent these collapses. HO atoms
have no VDW radii in the standard Amber force field.
> On Mon, Mar 28, 2011 at 3:29 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hi,
> >
> > Just a few comments:
> >
> > On Mon, Mar 28, 2011 at 12:05 PM, Hashem Taha <htahaphd.gmail.com>
> wrote:
> >
> > > I am trying to simulate a peptide with the following sequence:
> > >
> > > p = sequence { VAL PRO ILE VAL THR PTR ALA ALA NHE }
> > >
> >
> > What is PTR? Some phosphorylated amino acid? (threonine, tyrosine?)
> >
> >
> > >
> > > initial minimization of the peptide completed with no problems.
> However,
> > > when I try to heat the molecule using the following input (see below),
> > the
> > > simulation completes, but the temperature goes completely out of whack.
> > The
> > > peptide falls apart upon heating. The first few steps are OK, but at
> > around
> > > NSTEP=1000, the temperature rises to 2519.20 K and gets progressively
> > > higher.
> > >
> > > I have attempted this heating phase with both implicit (both igb=1 and
> > > igb=2) and explicit solvents (tip3p water), as well as different
> > > thermostats
> > > (both Langevin and Berendsen), and all of these attempts gave the same
> > > result. The temperature would increase to a ridiculous value and the
> > > peptide
> > > would break apart. I've also attempted different cutoff values (cut=16
> > and
> > > cut=999).
> > >
> > > Could you please provide some feedback as to what this problem could
> be.
> > > Here's a sample input for my heating protocol. The bolded parts are
> what
> > I
> > > modified!
> > >
> > > md run-T raise
> > > &cntrl
> > > imin=0, irest=0, ntx=1,
> > > nstlim=10000, dt=0.0005,
> > >
> >
> > This is quite a small timestep, so it's probably fair to say it's not an
> > integration error.
> >
> > ntc=2, ntf=2,
> > > *ntt=1, tautp=1.0,*
> > > tempi=0., temp0=300.0,
> > > *igb=1, ntb=0,*
> > > *cut=999.0*,
> > > ntwe=25, ntwx=25, ntpr=25,
> > > &end
> > > &wt
> > > type='TEMP0', istep1=0, istep2=1000, value1=0.0, value2=30.0,
> > > &end
> > > &wt
> > > type='TEMP0', istep1=1001, istep2=2000, value1=30.0, value2=60.0,
> > > &end
> > > &wt
> > > type='TEMP0', istep1=2001, istep2=3000, value1=60.0, value2=90.0,
> > > &end
> > > &wt
> > > type='TEMP0', istep1=3001, istep2=4000, value1=90.0, value2=120.0,
> > > &end
> > > &wt
> > > type='TEMP0', istep1=4001, istep2=5000, value1=120.0, value2=150.0,
> > > &end
> > > &wt
> > > type='TEMP0', istep1=5001, istep2=6000, value1=150.0, value2=180.0,
> > > &end
> > > &wt
> > > type='TEMP0', istep1=6001, istep2=7000, value1=180.0, value2=210.0,
> > > &end
> > > &wt
> > > type='TEMP0', istep1=7001, istep2=8000, value1=210.0, value2=240.0,
> > > &end
> > > &wt
> > > type='TEMP0', istep1=8001, istep2=9000, value1=240.0, value2=270.0,
> > > &end
> > > &wt
> > > type='TEMP0', istep1=9001, istep2=10000, value1=270.0, value2=300.0,
> > > &end
> > >
> >
> > This is overkill. You would get exactly the same result if you used
> >
> > &wt
> > type='TEMP0', istep1=0, istep2=10000, value1=0.0, value2=300.0
> > &end
> >
> > since it linearly interpolates the temperature. I don't know that this
> > would fix things, but it's worth a try if you haven't already. Another
> > useful approach is to visualize what's happening (specifically try to see
> > if
> > a hydrogen atom is collapsing into another atom, such as an oxygen or
> > something). This is especially more likely with phosphate groups.
> >
> > Hope this helps,
> > Jason
> >
> > &wt
> > > type='END'
> > > &end
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Mar 28 2011 - 13:30:06 PDT
