On 06/01/2025 15:47, Dulal Mondal via AMBER wrote:
> Thank you sir for your response. I already run conventional MD. Then I
> calculate the average dihedral and potential energy. Then I run the aMD
> simulation. My system is metallo protein human carbonic anhydrase II in
> water. When I set iamd=2 and include the dihedral parameters the system is
> stable. But when I put the potential energy parameter the system breaks.
> Thanking You
Your system is probably too big for an off-the-shelf application of aMD. If you absolutely must use it, try to decrease the boost, which could give you more stability. Additionally, it should also
decrease the energy noise in the results. Related to this, don't forget that you will have to reweigh the results, which is going to give you two types of issues. The first is that you have to make
sure the results have converged, and this may well take a while, depending on the natural conformational landscape of your system. The second is that the reweighing involves exponentiation of numbers
over potentially multiple orders of magnitude. Thus, if you implement this naively, the numerical errors are going to be so large that the final results are going to be more or less meaningless. This
is particularly important for a system as large as yours, even though, in my personal experience, I had to use *a lot* of care in reweighing results from a peptide as small as 16 residues. So, my
suggestion is that, before you continue with this method, you should make sure you are comfortable in implementing your own reweighing code, using at the very least logarithmic sums and an arbitrary
precision library.
Cheers,
Charo
--
Dr. Charo I. del Genio
Institute of Smart Agriculture for Safe and Functional Foods and Supplements
Trakia University
Stara Zagora 6000
Bulgaria
https://charodelgenio.weebly.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 06 2025 - 06:30:02 PST
