PC GAMESS/Firefly-related discussion club

Learn how to ask questions correctly

Jim Kress
jimkress_35@kressworks.com

A far as a solvent (e.g. water) the UFF force field includes the parameters for TIP3 water and can be used in the QMMM simulation.

What are you trying to calculate?

Jim


On Tue Feb 10 '09 6:50pm, Raul Mera wrote
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>Jim,

>I'm not really sure about how many atoms would I need, but only the protein has around 2500. Considering a box of solvent (water + ions), I think I would need something like 10.000 atoms (and a fellow grad student in my lab who would also use Firefly has a system much bigger).

>I also think that point charges alone would be a bad approximation for the protein if I want to carry optimization, but I was thinking about using other program for the qmmm optimization and then Firefly only for the single point, and subsequent wave function analyses. I remember that for a single point calculation the only "MM" effect taken into account in an electrostatic embedding are the point charges of the force field. Please correct me if I am wrong.

>Thanks you very much for your help,

>Raul

>On Tue Feb 10 '09 4:40pm, Jim Kress wrote
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>>Raul,

>>The latest version of Firefly has no QM/MM capability.  Version 6.4 of PCGAMESS does and yes, it is still limited to 3500 atoms.

>>What number of atoms do you need for your calculation?

>>Yes, you can run a calculation with point charges using the current version of Firefly.  However, you will lose the bonding attributes at the edges of your molecule/ cluster/ whatever and will only incorporate polarization effects due to the point charges.

>>For large systems where long range forces can be adequately modeled by point charges, that may be a reasonable approach.

>>Jim Kress
>>
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