[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units
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.
That's what it was. Thanks a bunch. A follow-up question:
Gromacs Manual, page 142 in Chapter 7, Run parameters and Programs:
When you want to use LJ correction, make sure
that rvdw corresponds to the cut-off in
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.
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