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

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Fri Apr 6 03:29:34 CEST 2007

Yes. I did this way. I wrote it in small awk script. If you like I can
share with it.

Best regards
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive  Singapore 637551 Tel: +65-63162885 Fax: +65-67913856

-----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

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 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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