[gmx-users] Velocities with constraints

[Mark Abraham]

Hi,

Sounds right. Otherwise, the algorithm involved is SETTLE or RATTLE, which
has an analytic solution, not LINCS.

Mark

On Wed, Nov 11, 2015 at 10:31 PM Caro Miguel <miguel.caro at aalto.fi> wrote:

> I'm realizing now that the equations I'm using assume rotation about an
> axis that goes through the center of mass, which needs not be the case
> during the dynamics. This is probably the origin of the problem.
>
> Regards,
> Miguel
>
> --
> Dr. Miguel Caro
> Postdoctoral researcher
> Department of Electrical Engineering and Automation, and
> COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Email: mcaroba at gmail.com
> Work: miguel.caro at aalto.fi
> Website: http://mcaroba.dyndns.org
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Miguel
> Caro [miguel.caro at aalto.fi]
> Sent: 11 November 2015 20:37
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Velocities with constraints
>
> Dear Gromacs users,
>
> I am using the rigid water model TIP3P and running some dynamics. I need
> very accurate velocities from the output trajectory. When I do frequency
> decomposition of these velocities, I see that there is a non-negligible
> vibrational component to them, that is, the atomic velocities of the
> molecules are not following exactly the constraints given for a rigid
> body. What I mean by this is that the velocities are not fully
> consistent with what should be expected from a rigid body rotating about
> an instantaneous rotation axis (plus a center of mass translation).
>
> I have trying debugging my code but haven't been able to find any
> mistakes, hence my question: is this behavior to be expected from
> Gromacs and can it be influenced for instance by tuning the LINCS
> parameters?
>
> Many thanks for your help,
> Miguel
> --
> *Dr. Miguel Caro*
> /Postdoctoral researcher/
> Department of Electrical Engineering and Automation,
> and COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Personal email: *mcaroba at gmail.com*
> Work: *miguel.caro at aalto.fi*
> Website: http://mcaroba.dyndns.org
> --
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