[gmx-users] Re: Parameterizing a force field (Mark Abraham)

Lee-Ping leeping at MIT.EDU
Thu May 10 22:46:44 CEST 2007

Thank you both for the response!  I looked at the -j option in mdrun,
but it looks like that has about as much documentation as ffscan (i.e.
none at all).  I also fruitlessly checked the mailing list archives for
the past year and a half; there are some questions about ffscan, but
none of which contained instructions on how to run it.  

The next step is to look inside the gromacs source code, but there are a
lot of different files and I'm not sure as to which pieces of source
code describe how the input files are parsed.  If you could tell me
which files to look at, I would appreciate it a lot.  Thanks again!

1) What piece of code do I look at to see how mdrun parses the wham.gct
file (turned on by the -j switch)?
2) Which file describes how ffscan parses its inputs?

Also: If ffscan performs a grid scan, is it really able to fit 100+
parameters in a reasonable period of time (couple of hours)?  Would a
numerical optimization procedure for the parameters be a possible
improvement over this?

- Lee-Ping

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