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
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--
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 - 12:30:06 PDT
