[gmx-users] Tabulated potentials make newbies crazy
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
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
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:
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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