[gmx-users] Tabulated potentials make newbies crazy

ms devicerandom at gmail.com
Fri Nov 27 20:53:14 CET 2009


I am really having a hard time figuring out how to use tabulated
potentials correctly.

In general, the information on how to use tables is sparse and scattered
in several points of the manual (ch.5, ch.7, ch.6.7...) -I hope to write
a short howto in the wiki once I get this working, but now I really
don't know what to do.

This is the story, sorry if it is long, but...:

My problem is conceptually simple:I want to use a tabulated potential
for the Calpha in my protein chain,to build a CG model.

I want the Calpha to use the tabulated potential,both between themselves
and with other atoms, and I want other atoms to behave between
themselves just as before (or at least as possible as close as before,
at least for now).

I first tried therefore to put C-alpha in the energy groups, called the
table table_C-alpha_C-alpha.xvg, vdw=user , and there it complains
because one atom cannot belong to two energy groups (C-alpha and
Protein) at the same time.

Just to try, therefore, I removed all occurences of energy groups in a
.ndx files, except for system and C-alpha (I have no solvent). And there
it complains that atoms belong to different energy groups, but belong to
the same charge group.

I understand therefore that energy groups and charge groups must be
identically defined.

Anyway, just for the sake of learning how to get gmx use a tabulated
potential, I apply the tabulated potential to all the peptide chain,
(and I rename the table table_protein_protein.xvg). At this point, it
stops asking me for a "table.xvg" file. I realize that it probably wants
to know how to define other non bonded interaction. Since there is only
the protein, I rename the table_protein_protein.xvg as table.xvg and retry.

And now I cry because mdrun doesn't start, telling me:

   Fatal error:
   Out of range force value 2.44081e+41 in file 'table.xvg'

The "out of range force value" error does not appear at all on google. I
understand it's "kinda high" - but it's a very steep repulsion and so it
is naturally like that at distances close to 0.

Now, my questions are:
- What is the accepted range of values in tables?
- How do I define a steep repulsion potential correctly?
- Is there a way to define a table for specific atoms in a chain,
leaving the other atoms using the standard VdW potential? I guess it
requires splitting the chain in two energy groups, but I don't
understand if it a)makes sense/creates problems b)how to deal with the
fact that the chain should be a single charge group.

Thanks to everyone!

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