From: Cole Gleason (cole_at_colegleason.com)
Date: Tue Oct 19 2010 - 13:53:17 CDT
On Mon, Oct 18, 2010 at 10:12 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Mon, Oct 18, 2010 at 10:24 PM, Cole Gleason <cole_at_colegleason.com> wrote:
>> On Mon, Oct 18, 2010 at 8:20 PM, Nicholas Musolino <musolino_at_mit.edu> wrote:
>>> Alex K. has provided some super-helpful information, as always, about using tabulated potential functions.
>>> I just wanted to check in and ask, are you sure that you (and your professor) are on the same page about what it takes to recompile NAMD? It's possible he's used to bigger (more complicated) software projects that spend a very long while for compile time.
> the compile time really isn't so much of an issue. the abysmal performance
> of interfacing a hand written fortran90 parser into c++ code would be
> a major PITA.
> why not write a little fortran wrapper around it to first generate the tables
> and then run the MD code using them. that is how i would introduce
> a generic parser into an MD code.
This is the method we have decided upon. Just so I understand what is
going on here, we write a wrapper that takes a function and then uses
that function to generate tabuated output. NAMD then reads this
tabulated output instead of it's internal functions. To do that we
need to hack the NAMD code to support reading functions from tables.
Then we can run NAMD simulations by specifying a table to read from,
I might do this on my own just so I understand the functions better
and what interactions are really at play here.
>> Cole Gleason
>> Student, Marmion Academy
>> Email: cole_at_colegleason.com
>> Website: colegleason.com
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
-- Cole Gleason ---------------------- Student, Marmion Academy Email: cole_at_colegleason.com Website: colegleason.com -- Cole Gleason ---------------------- Student, Marmion Academy Email: cole_at_colegleason.com Website: colegleason.com
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