[gmx-users] Fwd: QMMM calculation

Pradip Kumar Biswas p.biswas at csuohio.edu
Sat Jun 17 18:38:50 CEST 2006

Begin forwarded message:

> From: amit at mbu.iisc.ernet.in
> Date: June 17, 2006 2:53:27 AM EDT
> To: "Pradip Kumar Biswas" <p.biswas at csuohio.edu>
> Subject: Re: QMMM calculation
> Dear Sir,
> Thank you for your kind reply. Which force field should I use for my
> calculation. I have seen you using OPLS for your calculation. Is it
> possible to use Gromos force field, where polar hydrogen is used.

You should be able to use any force field implemented or supported by 
Gromacs. QM/MM does not depend upon the force field.

> If all
> atom force field in not taken, then no of atoms will reduce in CPMD 
> for QM
> calculation.

I could not really get what you mean. The number of QM atoms in CPMD 
will be coming from the [QM] section of the index.ndx file of Gromacs. 
First you need to create an index.ndx file in the usual Gromacs way and 
then manually add the [QM] section where you mention your desired atom 
ids. The rest of the atoms of your system will go to CPMD as an 
external field where you can manipulate their number by setting up a 
qmmmcoulomb_cutoff (pl. see the other posting today).

> I am facing problem in generating the gro & itp files for my ligands in
> OPLS force field.
> Please figure out the way for generating parameters file for my
> non-standard residue using OPLS FF.

If you are comfortable with Gromos FF, go ahead with that.

> Thanking you,
> with regards,
> amit

Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
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