[gmx-users] TIP4ew water and velocities on dummy atoms

Mark Abraham mark.j.abraham at gmail.com
Sun Jan 19 11:29:39 CET 2014


That does sound strange. Does gmxcheck show that the original .trr has

On Jan 19, 2014 2:16 AM, "Antila Hanne" <hanne.antila at aalto.fi> wrote:

> Dear experts,
> I converted a trajectory (.trr) containing a simulation of tip4ew water
>  to .gro format. In the resulting .gro file, there are velocities also for
> the tip4 virtual sites MW. This confuses me, since these sites have no
> mass. How is this velocity calculated? I have been under the impression
> that, at each step, the coordinates of MW are merely assigned based on the
> coordinates of the rest of the water atoms.
> Help will be appreciated!
> Yours,
> Hanne Antila
> PhD candidate,
> Aalto University
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