[gmx-users] Velocities with constraints

[Caro Miguel]

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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