[gmx-users] User-defined potentials.
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 28 18:02:45 CET 2001
On Tue, 27 Nov 2001, Ram'on Garc'ia Fern'andez wrote:
>Could you give me some help about the usage of user-defined potentials?
Have a look in the gromacs 3.0 paper. You need a single file
with 7 columns of data. You have in the distribution (e.g. in file
>It seems that the HTML manual is not quite uptodate. It says that two
>files, d???.xvg and r???.xvg have to be created, but according to the
>source code this is not the case.
Use the source...
>I understand that I need to pass a command line option -table with the
>filename that contains the user-defined potential. That file contains
>in the columns the coulombic and van der Waals potentials. However,
>how can I make a potential different for each pair of atom types?
>I suppose that the user defined potential is not automatically applied
>to all pairs of any type of atoms.
Yes it is. Your only variation is the force field parameters.
>Another question: what is the meaning of rvdw_switch? Does it mean that
>for distancer lower that this one, vdw = 0?
Only important for shifting and switching functions. See printed manual.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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