[AMBER] How to avoid SHAKE on a specific QM hydrogen atom in QM/MM simulations without compromising qmshake=1 flag

From: Amit, Amit \(amit.amit--- via AMBER <"Amit,>
Date: Thu, 21 Jul 2022 10:38:52 +0000

Dear Amber Community,

I hope you all are safe and healthy,

Please help me for : How to avoid SHAKE on a specific QM atom in QM/MM simulations?

I tried "noshakemask=.12" flag but than sander asked for "qmshake=0". I don't want to avoid SHAKE for all of my QM atoms, instead I want to avoid SHAKE only for a specific H atom, that is being transferred from atom A to B. Aim is to capture the energy barrier for hydride transfer, and for that I don't want to restrain this particular bond involve this H atom.

Any suggestions or experience regarding this would be highly appreciated.

Thank you very much in advance!

Amit Singh MSc
Doctoral Researcher
Institute of Molecular Biosciences
Karl-Franzens-University Graz
Humboldtstrasse 50/3 e-mail: amit.amit.uni-graz.at<mailto:amit.amit.uni-graz.at>
A-8010 Graz Mobile: (+43 688) 640 648 38
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Received on Thu Aug 04 2022 - 13:35:18 PDT
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