[gmx-users] using SETTLE for constraints
Mark.Abraham at anu.edu.au
Mon Sep 7 10:28:05 CEST 2009
Dmitri Dubov wrote:
> Dear GMX'ers,
> I am confused with some basic questions about using SETTLE constraining algorithm in gromacs.
> 1) This solution of SHAKE is used, particularly, for spc water. So spc.itp file contains the [ settles ] section, and there is no another [ constraints ] within it. But the parameter "constraint-algorithm" in /water/grompp.mdp (see the gromacs native tutorial for spc water simulation) is set to "Lincs". What is the REAL treatment of water constraints in this case?
GROMACS transparently uses the best constraint algorithm that you allow
it use on a given molecule. The only way you can *not* use constraints
on water with the standard water .itp files is to #define FLEXIBLE, as
you will see in those .itp files. Since settle is specified there it is
The choice of LINCS or SHAKE pertains only to molecules for which there
is no other constraint option. You can verify this by doing a quick
simulation of pure water specifying either of the above and seeing that
the results are identical. IIRC the .log file makes a note of what
constraints are being used.
> 2) From manual the run parameter "constraint-algorithm" has only two (LINCS or SHAKE) alternatives. How can I specify the SETTLE using?
See above. Looking for SETTLE in the manual index would have helped :-)
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