[gmx-users] tabulated potentials and pairs

Berk Hess gmx3 at hotmail.com
Tue Jul 29 11:46:09 CEST 2008


The scaling in Gromacs is performed on the prefactor 1/(4 pi eps0 eps),
so you do not need to do this in the tables.

BTW you do not need to copy the table, you can also soft-link it,
or give the same file name for both table options.


> Date: Fri, 25 Jul 2008 11:19:21 -0700
> From: mbx0009 at yahoo.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] tabulated potentials and pairs
> Dear all,
> I simulate a protein in water, and use AMBER03 parameters plus a tabulated 
> potential for the Coulomb interactions. Next to the table.xvg file that i provide, 
> mdrun seems to require a second file called tablep.xvg, which is supposed to 
> contain the corrsponding tabulated pair interactions.
> For now I just copied table.xvg to tablep.xvg, and that seems to work, 
> but I wonder if for the pairs that are defined in my topology file (from
> grompp) Coulomb interactions will be scaled automatically, 
> or whether I have to scale the values in tablep.xvg myself ??
> (I understand AMBER03 scales Coulomb 1-4 interactions by a factor 0.8333)
> thanks in advance for any help!
> Michael
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