Re: Colvars Orientation Question

From: Giacomo Fiorin (
Date: Wed Jul 10 2019 - 13:28:16 CDT

Hi Xander, it looks like the initial conditions are not near the energy
minimum of the restraint, making the force exceedingly large.

One option may be to initializing the restraint centers near the initial
conditions, and then move them to the value that you need. Alternatively,
you can keep the restraint centers as they are, but change the force
constant over time. For example, starting at 1/1000 of the force constant
that you have now, and gradually switch it up (using targetForceConstant).


On Wed, Jul 10, 2019 at 2:20 PM Xander Gonzalez <>

> ---------- Forwarded message ---------
> From: Xander Gonzalez <>
> Date: Tue, Jul 9, 2019 at 3:54 PM
> Subject: Re: namd-l: Colvars Orientation Question
> To: Jérôme Hénin <>
> Thank you again for your advice, I did this and am receiving large values
> for the energy, around 10^4. I am also receiving large values for the force
> quaternions, around 10^4 again. Do you have any further advice for
> continuing?
> Regards,
> Alexander
> On Tue, Jul 9, 2019 at 4:49 AM Jérôme Hénin <> wrote:
>> Hi Alexander,
>> To get a full view of the process, you can enable outputEnergy for the
>> harmonic bias and outputAppliedForce for the collective variables. If the
>> deviations are large you should see high energies and forces.
>> Best,
>> Jerome
>> On Fri, 5 Jul 2019 at 21:23, Xander Gonzalez <>
>> wrote:
>>> Thank you for the response. I have checked the colvars.traj file and the
>>> beginning quaternions are significantly different than the center colvars
>>> set in the configuration file, and the final quaternions are different than
>>> the target centers. I also visualized the rotations with the script you
>>> sent, it seems like the initial rotation is caused by the second collective
>>> variable rotating about 90 degrees. I have tried setting the target center
>>> for the second colvar quaternion to be the same as it's center to see if
>>> this would keep this rotation from happening, but I get the same result--000000000000696f51058d57d994--

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