Re: Rigid bonds and non-bonded energy

From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Tue Oct 20 2015 - 10:33:51 CDT

"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
email: radak_at_uchicago.edu

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