From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Aug 05 2014 - 14:29:22 CDT
Two questions:
(1) knowing that computers don't have infinite precision, there will
*always* be small deviations. The question to ask is: are they significant?
(2) Did you plot the same distribution for an MC simulation? Because I see
no fundamental reason the distribution of rigid bond lengths in MD should
have a higher sigma than MC. Sure, one can add rigid body rotations to an
MC move set, but one could also implement rigid bodies in MD (albeit at
the cost of increased complexity). Conversely, one could conceivably use
something similar to SHAKE in MC. SHAKE essentially just calculates the
rigid body translation and rotation numerically (as opposed to analytically).
On 08/05/2014 03:10 PM, Hadi wrote:
> Kenno,
>
> In general, I think it is fair to say that unlike MC simulations, the
> rigid models in MD simulations are only slightly flexible considering the
> algorithm, rigid tolerance, time step, etc. that will be used. I have
> plotted the histogram of bond length for a given model with appropriate
> parameters and observed that the distribution of bond length has some
> small deviations from a delta function.
>
> Hadi
>
>
> On Tue, Aug 5, 2014 at 11:41 AM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
>
> That doesn't mean the model wouldn't be rigid, just that the
> temperature wouldn't be right. More importantly, I don't think the
> person who asked the original question is planning to perform Langevin
> integration. Langevin is good to mimic the effects of solvent
> collisions when running implicit solvent and can also be used to
> improve sampling in some instances, bit it wouldn't be very
> appropriate for his purpose. The gold standard for explicit solvent
> simulations with CHARMM is Verlet (and that's also what was used to
> parametrize the force field).
>
>
> On 08/05/2014 12:52 PM, Hadi Dinpajooh wrote:
>
> Well, as mentioned in the link NAMD is not well developed if one uses
> rigid models and Langevin integration:
>
> " ... Although /NAMD/ will run with Langevin integration and rigid
> bonds
>
> both active, the equilibrium temperature of the system does not
> converge
> to the correct value. Different Langevin equations are needed to
> produce
> the correct velocity distribution, which have not yet been added
> to /NAMD/."
>
>
> Hadi
>
> Sent from my iPhone
>
> On Aug 5, 2014, at 7:54 AM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>
> <mailto:kvanomme_at_rx.umaryland.__edu
> <mailto:kvanomme_at_rx.umaryland.edu>>> wrote:
>
> On 08/05/2014 03:14 AM, Hadi wrote:
>
> (2) It is my understanding that the parameters you
> copy-pasted into
> your e-mail are just "reasonable values" for in case
> an MD engine or
> methodology is used that does not support rigid water.
> They won't give
> the exact same properties as the true rigid TIP3P
> model. NAMD,
> however, does support rigid water; assuming the psf is
> generated
> correctly, all one need to do is put the following
> line in the NAMD
> input:
> rigidBonds water
> Though if you're using the CHARMM force field, it's
> actually
> recommended to instead use
> rigidBonds all
> because that's what the force field is parametrized for.
>
>
> I hope it is clear that unlike MC simulations, a rigid
> model can actually
> be slightly flexible in MD simulations.
>
> Hadi
>
>
> Umm no, provided that no mistakes were made in the set-up of SHAKE
> (rigidBonds in NAMD), a rigid model is really rigid in MD.
> Except for
> insignificant numerical deviations related to the SHAKE
> tolerance. More
> info here:
> http://www.ks.uiuc.edu/__Research/namd/1.5/ug/node64.__html
> <http://www.ks.uiuc.edu/Research/namd/1.5/ug/node64.html>
>
>
>
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