[gmx-users] Fwd: QMMM simulation
Pradip Kumar Biswas
p.biswas at csuohio.edu
Thu Jul 20 23:33:55 CEST 2006
Begin forwarded message:
> From: amit at mbu.iisc.ernet.in
> Date: July 20, 2006 5:03:34 PM EDT
> To: "Pradip Kumar Biswas" <p.biswas at csuohio.edu>
> Subject: QMMM simulation
> Dear Sir,
> While running mdrun for normal MD for the system at 300K, I am getting
> following error
> "ODIIS| Insufficient progress; reset!"
This is not an error message but a progress report. You can take a
look at the CPMD manual.
> Now I am using PCG MINIMIZE for the same run. Pls correct me if I am
That is what you should do. PCG minimize is quite robust and 'almost'
certain to work where DIIS minimizer fails. The failure of DIIS depends
on the system.
> I am doing QMMM simulation for protein along with ligands. Two ligands
> the protein cavity reacting with each other along with MG2+ to form
> products and also some water is taking part in the reaction. I have
> ligands and Mg atoms as QM atoms.
Where did you get the VDB pseudopotentials for the Mg atoms? Or, are
you using any norm conserving PP?
> But I have not taken any water as QM
> atoms. How to incorporate water in the reaction as I dont know which
> is interacting in the reaction.
May be the Gromacs community might help you better here but I trust
that you have to guess/judge which water molecule(s) might take part in
the reaction and include that(them) in the QM. You should monitor your
output frames time to time to see which water are coming closer to the
active site and which are going away. Accordingly, if you find you have
chosen a wrong water for the QM, you can stop and restart your MD
simulation by putting the right water in the QM.
Hope, this would help. If you feel unhappy with the time requirement
with the PCG minimize, I'll send you a very small patch with which you
can use PCG minimize for the first time but use DIIS for all subsequent
steps (DIIS is way faster than PCG). To get a good wavefunction is the
key and using PCG only once does help.
> with regards,
Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
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