[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

Frankie Montenegro frankie.montenegro at gmail.com
Tue Jul 17 09:41:46 CEST 2007

> So if you box size is 5 (as you say) and your cut-off is 1, then you
> should not get an error.
> So one of the two things is wrong.
> Maybe you made a pdb file with box 5?
> pdb is in Angstrom, while Gromacs uses nm, so there is a conversion
> factor of 0.1.
> Berk.

That's what it was. Thanks a bunch. A follow-up question:

Gromacs Manual, page 142 in Chapter 7, Run parameters and Programs:

                vdwtype: User
                               When you want to use LJ correction, make sure
                               that rvdw corresponds to the cut-off in
the user-defined

End of quote.

But my potential has three different vdw cutoffs for three different
 Is there a way to account for all of them?

If not,  I want to set it to the greatest one, correct? I can't see
that option having any unwanted consequences, assuming first column of
table.xvg, table_ii_ii.xvg and table_jj_jj.xvg stays within rvdw+1.

Thanks again,

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