[gmx-users] modify C6 directly in FF using sigma and epsilon

[David Mobley]

Sure, that would be great!

David


On 4/5/07, Mu Yuguang (Dr) <YGMu at ntu.edu.sg> wrote:
> Yes. I did this way. I wrote it in small awk script. If you like I can
> share with it.
>
> Best regards
> Yuguang
>
> Dr. Yuguang Mu
> Assistant Professor
> School of Biological Sciences
> Nanyang Technological University
> 60 Nanyang Drive  Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
> http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
> Sent: Friday, April 06, 2007 4:11 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] modify C6 directly in FF using sigma and
> epsilon
>
> David Mobley wrote:
> > David,
> >
> > I'm using 3.3/3.3.1.
> >
> > Is there an easy tweak to the source code that would allow something
> > like this? i.e. could I somehow easily tweak the bit where it reads
> > the nonbond_params section so I can use an alternate combination rule
> > there by specifying, say, a different nonbonded parameter type?
> >
> It doesn't look like it.
> The sigma and epsilon are first read in the atomtypes section, and a
> matrix is filled in with sigma and epsilon. Then, if you overwrite a
> pair in the nonbond_types section two (because f symmetry) matrix
> elements are replaced. Finally, just before writing the file the values
> are converted to C6 and C12.
>
> It seems that your best bet is to write that little Perl script to
> convert the whole force field to C6/C12.
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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