On Tue, Dec 22, 2009, "Frank X. Vázquez" wrote:
>
> I would like to output the Van der Waals and electrostatic forces for
> every atom using Sander. Because I need the forces at every time step, I
> would like to just have Sander write the forces I need to a file for
> processing later. Could somebody please tell me where I can find the Van
> de Waals and and electrostatic force calculations, and what array would
> I need to write to file? Also, can I use the force arrays as is, or do I
> need to rearrange the values somehow?
This is not a simple task. The total force is assembled into an array called
"f" in force.f. But the electrostatic contributions are added in two parts
(the so-called "direct" and "reciprocal" contributions), and combined with
the van der Waals and all other contributions in this one array. You can look
at force.f to see how most things are assembled (look for the comment line,
'calculate the non-bonded forces'); I guess you would then go into the
short_ene routine to get the vdw terms, and see how the electrostatic forces
are assembled, writing code to collect and output the information you
need. Basically, you will need to really learn your way around the code (not
all that hard, actually, but not simple to explain in an email, either).
...dac
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Received on Wed Dec 23 2009 - 19:00:04 PST
