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From: Carlos Simmerling <carlos.simmerling.gmail.com>

Date: Tue, 16 Mar 2010 19:09:24 -0400

this is missing the point. It's not that the equation is wrong, its that

it's more complex than the equation indicates, or can be made to simply

indicate. There is 1-4 scaling, and excluded atom lists, and multiple phases

for dihedrals, and skipping duplication of 1-4s in rings, and so on. The

equation gives the basics, but the actual calculation involves significant

logic checking and checking various arrays that are built based on knowledge

of the topology of the system, not just coordinates. The equation as listed

doesn't even work for methane. There is no simple way to "correct" it,

though; one needs to understand the logic behind the force field, not just

the parameters.

On Tue, Mar 16, 2010 at 5:30 PM, Whimsica.aol.com <whimsica.aol.com> wrote:

*> I would be much more comfortable with a corrected Amber equation if one
*

*> exists that is good enough for simulating just nucleic acids for k12
*

*> students.
*

*>
*

*>
*

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Received on Tue Mar 16 2010 - 16:30:02 PDT

Date: Tue, 16 Mar 2010 19:09:24 -0400

this is missing the point. It's not that the equation is wrong, its that

it's more complex than the equation indicates, or can be made to simply

indicate. There is 1-4 scaling, and excluded atom lists, and multiple phases

for dihedrals, and skipping duplication of 1-4s in rings, and so on. The

equation gives the basics, but the actual calculation involves significant

logic checking and checking various arrays that are built based on knowledge

of the topology of the system, not just coordinates. The equation as listed

doesn't even work for methane. There is no simple way to "correct" it,

though; one needs to understand the logic behind the force field, not just

the parameters.

On Tue, Mar 16, 2010 at 5:30 PM, Whimsica.aol.com <whimsica.aol.com> wrote:

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Received on Tue Mar 16 2010 - 16:30:02 PDT

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