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:
Quote:
vdwtype: User
When you want to use LJ correction, make sure
that rvdw corresponds to the cut-off in
the user-defined
function.
End of quote.
But my potential has three different vdw cutoffs for three different
interaction.
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,
Frankie
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