Begin forwarded message:
From: [EMAIL PROTECTED]
Date: July 20, 2006 5:03:34 PM EDT
To: "Pradip Kumar Biswas" <[EMAIL PROTECTED]>
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 wrong.
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 in
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 taken
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 water
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,--
amit
Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
http://comppsi.csuohio.edu/groups/people/biswas.html
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