[gmx-users] about sa_surface_tension
per.larsson at sbc.su.se
Mon Oct 18 14:40:05 CEST 2010
This is unfortunately a bit confusing, but prior to the release of 4.5.2 gromacs did not use the value of
the sa_surface_tension that was specified in the mdp-file. It was always set to 2.092, and then hardcode to take a certain
value (other than 2.092) depending on the GB-model.
2.25936 is the value used together with OBC/HCT models, it is slightly lower with the Still model.
In 4.5.2 the default will be -1, which, if left unchanged, will be changed to proper values (and a note written about this).
The effect on the result will be very small, since the sa_surface_tension-parameter is only used for the non-polar part
of solvation, which in turn is a very minor part of the total force.
Also in 4.5.2, setting sa_surface_tension=0 means that no non-polar solvation is being calculated.
Sorry for the confusion
18 okt 2010 kl. 14.07 skrev Christian Mücksch:
> Dear all,
> when using implicit solvent models, the sa_surface_tension parameter is set to 2.092 kJ/mol/nm2 by default.
> However in Gromacs benchmarks with dihydrofolate reductase this parameter is set to 2.25936.
> Can someone please explain this parameter and in how far this would change the simulation outcome.
> Kind regards,
> Christian Mücksch
> Department of Physics
> TU Kaiserslautern
> Erwin Schrödinger Straße
> 67663 Kaiserslautern
> Phone: +49 (0)631 205 4287
> Email: muecksch at rhrk.uni-kl.de
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