[gmx-users] Velocities with constraints

[Miguel Caro]

Dear Mark,

I have rechecked that my equations should actually be correct: I am 
calculating the angular velocity in the reference frame where the center 
of mass is at rest, therefore for a rigid body the rotational axis in 
this frame should go through the center of mass.

I have done further analysis of the results and have found very 
systematic errors in the angle between the velocity and the position 
vector of the atoms belonging to the same molecule. This angle should 
always be 90 degrees for rotational motion, however Gromacs is giving 
slightly less (typically about 89.5 degrees). I have checked the effect 
of single/double precision to be negligible here. My interpretation of 
this result is that Gromacs is *estimating* what the velocity vector 
will look like some time after the instant in which the positions are 
calculated. If you try to picture this, I think Gromacs is printing r(t) 
and v(t+dt) on the same line for each atom.

Is this what is going on? If so, what is the value of dt and how can I 
prevent this behavior? If dt is the same as the integration time I could 
then load the positions at time = t together with the velocities 
*printed* at t-dt. Does this make sense?

Ideally I would like to induce the behavior that r(t) and v(t) are 
printed on the same line.

Regards,
Miguel

On 2015-11-12 00:05, Mark Abraham wrote:
> 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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-- 
*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