Re: [AMBER] Suggestions on crossing energy barrier to break strong HBs

From: David A Case <>
Date: Fri, 29 Jan 2021 22:06:00 -0500

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 Fri Jan 29 2021 - 19:30:02 PST
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