From: Oleksii Zdorevskyi (zdorevskyi_at_bitp.kiev.ua)
Date: Thu Aug 06 2020 - 05:15:26 CDT
Dear NAMD developers,
I am new in performing QM/MM simulations with Live Solvent and have some
issues that do not allow me to move on with my calculations. I was looking
for some information about it in google and I managed to find only the
description of the few options in the NAMD manual
(http://www.ks.uiuc.edu/Research/qmmm/). Unfortunately, this information
was not sufficient for me to understand and use the LSS properly. So I ask
you for a help to clarify some things.
In my config file (qm2.conf) I use the following options for LSS:
qmLiveSolventSel on
qmLSSFreq 20
qmLSSMode dist
qmLSSRef 1 P1 1
However, after a certain step I obtain the following error:
ERROR: The number of QM atoms received (31) is different than expected: 28
FATAL ERROR: Problems broadcasting QM atoms.: No such file or directory
or
ERROR: The number of QM atoms received (31) is different than expected: 28
FATAL ERROR: Problems broadcasting QM atoms.: Success
I also attempted to reduce qmLSSFreq as well as changing LSSMode from
"dist" to "COM" but this led to the same results.
So, at a certain step the program does not exchange some of the solvent
molecules to the classical?
Are these issues connected with the inappropriate choice of the QM
simulation region or it is just a bug of LSS in NAMD?
My simulation system is quite simple - hydrogen peroxide molecule (H2O2)
in a water box. My QM region is: H2O2+the surface of the water molecules
that are situated close to H2O2. As I understand it properly, solvent
molecules are not appointed in QM region automatically, and each water
molecule must be indicated manually in the corresponding qm-region file.
So I just make an appropriate selection in VMD for the all the molecules
which are situated for example in 3.5 Angstrom from H2O2 and appoint them
to the same QM region as H2O2 (beta column in file qm_atoms.pdb). Is it
the right way to define QM solvent molecules?
All the necessary simulation files I have uploaded here:
https://drive.google.com/file/d/1mR7P5TkH5s0g7Iq0mcSu_Wm1aF2ZjkWC/view?usp=sharing.
I will appreciate any help and information.
Best regards,
Oleksii
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