Re: Rigid bonds and non-bonded energy

From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Tue Oct 20 2015 - 12:52:34 CDT

Interesting, so these are systematic energy differences on the order of
0.1 kcal/mol; that does seem concerning. I assume you are using PME? The
same FFT settings? Does the agreement change/improve if you run on a
single core?

On 10/20/2015 11:09 AM, Grzegorz Nawrocki wrote:
> I play with a small box of water, i.e. about 2.5 nm edge. Generate an
> output structure with rigid bonds and use it as an input. Repeat this
> until input and output are exactly the same. The electrostatic and VDW
> energies are equal to -15731 and 29873.3 [kJ/mol], respectively. Then
> I turn off rigid bonds (input and output structures are always the
> same) and the energies are -15729.9 and 29872.9. This kind of
> difference I am talking about.
>
> 2015-10-20 11:33 GMT-04:00 Brian Radak <brian.radak.accts_at_gmail.com
> <mailto:brian.radak.accts_at_gmail.com>>:
>
> "Much more similar" still sounds a bit concerning to me. I can
> generally get matching to all precision given by NAMD (i.e 1e-4),
> although frequently that is for single molecules in vacuum.
> Perhaps the variability of multiple threads on a large structure
> could plausibly change things, although even then variation at
> 1e-3 is a bit concerning.
>
> The only time I've noticed trouble is that when reading in
> velocities the kinetic energy tends to drift by about ~0.1
> kcal/mol (although turning on/off constraints will also affect
> this due to changes in degrees of freedom); in any event, you are
> not doing this.
>
> Brian
>
>
> On 10/20/2015 10:11 AM, Grzegorz Nawrocki wrote:
>> 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,
>>
>> 2015-10-19 15:40 GMT-04:00 Brian Radak
>> <brian.radak.accts_at_gmail.com <mailto:brian.radak.accts_at_gmail.com>>:
>>
>> 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 <mailto: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
>> <mailto: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 <tel:773%2F834-2812>
>> email: radak_at_uchicago.edu <mailto: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 <tel:773%2F834-2812>
>> e-mail: radak_at_uchicago.edu <mailto:radak_at_uchicago.edu>
>>
>>
>>
>>
>> --
>> 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 <tel:773%2F834-2812>
> email: radak_at_uchicago.edu <mailto:radak_at_uchicago.edu>
>
>
>
>
> --
> 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

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