[gmx-users] Velocities with constraints

Miguel Caro miguel.caro at aalto.fi
Wed Nov 11 19:37:23 CET 2015

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 

Many thanks for your help,
*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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