On Thu, Oct 15, 2015, Ross Walker wrote:
>
> I only had a chance to quickly glance at this but I suspect the
> adjustment of the number of degrees of freedom for shake and the
> randomization of velocities is occurring in the wrong order. The degrees
> of freedom adjustment is in subroutine degcnt in degcnt.F90.
I think it is more complicated than this. I *think* one should randomize
velocities in the usual way (ignoring shake, and using the full number of
degrees of freedom); then use the equivalent of the rattle2() routine
(see sff.c in $AMBERHOME/AmberTools/src/sff) to remove the components of the
velocity along the SHAKEN bond directions. Then you can update the count of
the number of degrees of freedom.
I'd check to see if there is velocity randomization code in Tinker: that is
often the cleanest and best-commented code for fundamental MD-related tasks.
....dac
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Received on Thu Oct 15 2015 - 11:30:04 PDT
