[gmx-developers] Warnings

David van der Spoel spoel at xray.bmc.uu.se
Sat Aug 9 09:57:44 CEST 2008

Roland Schulz wrote:
> On Fri, Aug 8, 2008 at 3:14 PM, David van der Spoel 
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>     Roland Schulz wrote:
>         - DispCorr = no when using constant temperature. If I understand
>         it correct this should always be done in that case.
>     This is more like a force field issue. Some force fields have it,
>     others don't.
> I wasn't able to find a documentation or mail on the list for that. Do 
> you have a list which need it and which don't? Should we put it in the 
> force field file in the long run to make this less confusing?
It is more involved than this. Most force fields actually do not use 
these at all. For instance OPLS uses an energy correction in combination 
with a shift function. However, Jorgensen has never described the shift 
function in his papers (but I have, see below :)). In addition OPLS/AA 
was developed for Monte Carlo and hence the shift function they use is 
fine for energies but gives discontinuous forces. This is not to be 
recommended for MD. In other words, it is a mess. If you find a way of 
making it clearer please make a proposal.

For some background information on switch/shift fun:
David van der Spoel and Paul J. van Maaren: The origin of layer 
structure artifacts in simulation of liquid water J. Chem. Theor. Comp. 
2 pp. 1-11 (2006)

> One more thing I forgot in the last mail:
> It seems that grompp doesn't check that all the amino acids in the 
> topol.top and conf.gro actually exist in the aminoacid.dat and in the 
> force-field files. Pdb2Gmx will give an error, but if you use the wrong 
> folder for you GMXDATA and get other files without the aminoacid you 
> don't get an error/warning in the grompp step.
In principle grompp does not interpret your system, other than for 
generating automatic index entries. What will typically happen is that a 
residue is not found in the aminoacid.dat file and hence is put in the 
"rest" group for t coupling etc. If you know of a way to detect this, 
and hence give a more comprehensible warning/error message, that would 
be useful.

> Roland
> -- 
> Center for Molecular Biophysics ORNL/UT cmb.ornl.gov <http://cmb.ornl.gov>
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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