Hi,
Just to toss some ideas- if you're strictly interested in seeing the
cascade effect of breaking the heme bonds, the simplest way would be to
manually break them, ie move the heme in your pdb so it no longer can make
the hydrogen bonds. It's very brute force, but it gets the job done.
Or you could just run the system at a higher temperature (350, 370K), but
you might want to employ some tempering (REMD or simulated tempering)
scheme. There's also a pretty deep pool of literature for accelerated MD
methods (example, J Chem Phys. 2004 Jun 22;120(24):11919-29) that are keyed
towards crossing energy barriers.
Best,
Kenneth
On Sat, Jan 30, 2021 at 1:28 AM Amit Sharma (Asstt. Prof., MCARS) <
asharma4.jmi.ac.in> wrote:
> I am trying to replicate what is already done in one of the published works
> where it is shown through long amber simulation that these bond breaking
> happens.
>
> Although following exactly what is already done, I do not get to see the
> bond breaking in my case.
>
> Wrote to the authors, but no reply yet since longtime.....I thought why not
> I try forcing the system to break the bond and then see if further steps
> replicate or not.
>
>
>
> On Sat, Jan 30, 2021 at 8:39 AM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Sat, Jan 30, 2021, Amit Sharma (Asstt. Prof., MCARS) wrote:
> > >
> > >I am simulating a protein system in which a heme molecule is strongly
> > >hydrogen bonded (via 2 HB's) to one of the protein residues. These HB's
> > are
> > >expected to break during the course (around ~700 ns) of NPT run and
> shall
> > >lead to the further cascade of bond breaking/making in the protein.
> >
> > Why do you think the hydrogen bonds should break at some particular time?
> > Even if you have a good reason for thinking you know the rate constant,
> > in any particular simulation the actual time may be much shorter of much
> > longer than the average time. Brute force MD is not a very efficient
> > method
> > for studying kinetic processes on such long (by MD simulation standards)
> > time scales.
> >
> > And, it could well be that your estimate of the strength of the hydrogen
> > bonds in question is too low. Further, if you have to break both
> hydrogen
> > bonds in order to proceed further that could slow things down even more.
> >
> > >
> > > imin = 0, irest = 1, ntx = 7, ntb = 2,
> > > pres0 = 1.0, ntp = 1, taup = 0.5, gamma_ln = 1.0,
> > > cut = 8.0, ntr = 0, ntc = 2, ntf = 2,
> > > tempi = 298.0, temp0 = 298.0, ntt = 3
> >
> > These look pretty standard, and generally OK. Others on the list might
> be
> > able to suggest some "accelerated" technique that would allow particular
> > hydrogen bonds to break more rapidly.
> >
> > ....good luck....dac
> >
> >
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Received on Sat Jan 30 2021 - 17:30:02 PST
