Thank you very much David.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Amit Singh MSc
Doctoral Researcher
Institute of Molecular Biosciences
Karl-Franzens-University Graz
Humboldtstrasse 50/3 e-mail: amit.amit.uni-graz.at
A-8010 Graz Mobile: (+43 688) 640 648 38
AUSTRIA
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
________________________________________
From: David A Case <david.case.rutgers.edu>
Sent: 21 July 2022 14:27
To: Amit, Amit (amit.amit.uni-graz.at); AMBER Mailing List
Subject: Re: [AMBER] How to avoid SHAKE on a specific QM hydrogen atom in QM/MM simulations without compromising qmshake=1 flag
On Thu, Jul 21, 2022, Amit, Amit (amit.amit--- via AMBER wrote:
>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.
The manual implies, and the code agrees, that shaking hydrogens in the qm
region is an all-or-nothing proposition. You can't shake most of them, but
leave one out.
You could play with the code starting at line 782 of set.F90, removing the
test that qmmm_nml%qmshake == 0 (lines 798 and 806) and see if bad things
happen. Try a small system first, and critically examine what is going on.
Or, be conservative: if have a hydrogen that is being transfered, you might
want to have a 1 fs time step anyway, since the forces near the trasnfer
point might be changing very quickly.
...good luck...dac
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Received on Thu Aug 04 2022 - 13:35:22 PDT
