From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Mon Oct 19 2015 - 14:40:51 CDT
RATTLE is just the constraint algorithm used in NAMD (I believe just the
original SHAKE algorithm plus some extra stuff to handle velocities). After
RATTLE is applied the coordinates are reset such that they abide by the
constraints. If the constraints are already satisfied, then this will have
no effect.
The obvious thing to do here would be to turn off rigidBonds and then see
if the energies match. If they do, then you are probably seeing an effect
from constraints. This happens to me a lot when I build protons with psfgen
and they are either wrongly placed at the origin or given an non-ideal bond
length.
On Mon, Oct 19, 2015 at 9:22 AM, Grzegorz Nawrocki <aksonik_at_gmail.com>
wrote:
> Dear Brian,
> Thank you for the reply. Yes, the bonds have optimal lengths.
>
> I am running dynamics, but the input and output structure is the same. It
> means that coordinates don't change at all, that is confirmed by zero
> kinetic energy. Non-bonded interactions depend only on positions, so I
> should get exactly the same values. If the energy is neither of the input
> nor output structure, what is the structure that energy comes from? Could
> you please explain me what you mean by saying "rattle" or "coordinate
> resetting"?
>
> 2015-10-16 18:42 GMT-04:00 Brian Radak <brian.radak.accts_at_gmail.com>:
>
>> Is your structure generated in accord with those constraints? Since you
>> are running dynamics, I believe RATTLE will have a go at coordinate
>> resetting. In that case the energy you get will not be the energy of the
>> input structure if the constraints are not satisfied.
>>
>> On 10/16/2015 04:39 PM, Grzegorz Nawrocki wrote:
>>
>>> Dear NAMD users,
>>> I run simulation with number of steps equal to zero, since I want to
>>> calculate energy of a single structure. Log file says that kinetic energy
>>> is zero, that is fine, but non-bonded energies, both VDW and electrostatic,
>>> significantly depend on rigid bonds are turned on or off. How it is
>>> possible?
>>>
>>> Best regards,
>>> --
>>> Grzegorz Nawrocki
>>>
>>
>> --
>> Brian Radak
>> Postdoctoral Scholar
>> Gordon Center for Integrative Science, W323A
>> Department of Biochemistry & Molecular Biology
>> University of Chicago
>> 929 E. 57th St.
>> Chicago, IL 60637-1454
>> Tel: 773/834-2812
>> email: radak_at_uchicago.edu
>>
>
>
>
> --
> Grzegorz Nawrocki
>
-- Brian Radak Postdoctoral Scholar University of Chicago Department of Biochemistry & Molecular Biology Gordon Center for Integrative Science, W323A 929 E. 57th St. Chicago, IL 60637-1454 Tel: 773/834-2812 e-mail: radak_at_uchicago.edu
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