Re: Rigid bonds and non-bonded energy

From: Grzegorz Nawrocki (aksonik_at_gmail.com)
Date: Tue Oct 20 2015 - 10:11:42 CDT

Thank you Brian very much for the explanation. I hadn't known about
coordinates resetting and I was sure that analyse exactly the same
structure. Indeed, with rigid bonds output structure is slightly different
than input one. When I use the former as input and turn of rigid bonds the
non-bonded energies are much more similar.

Best regards,

> 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"?
>>
>>
>>> 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
>>>>
>>>
>>> --
>>> 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
>>>
>>
>>
>>
>> --
>> Grzegorz Nawrocki
>>
>
>
>
> --
> 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
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