**From:** Xiaohu Li (*xiaohu-li_at_northwestern.edu*)

**Date:** Fri May 04 2012 - 10:31:41 CDT

**Next message:**Hall McDull: "A question about the CHARMM force field"**Previous message:**Aron Broom: "Re: Umbrella sampling-reliability of results"**In reply to:**Jérôme Hénin: "Re: forces saved in forcedcd"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi, Jerome,

Thanks for you information.

In fact, after applying a very large harmonic constraint on the

COM of the slab, their relative position to the ion is quite stable. I

actually was not applying this harmonic constraint in the first place,

but observe some uniform shift of the slab when the ion is placed near

the surface.

So I do not think this the the problem in my case.

Xiaohu

On 05/04/2012 09:32 AM, Jérôme Hénin wrote:

*> Hi Xiaohu,
*

*>
*

*> Some of the issues you are having could be due to a bad reaction
*

*> coordinate. You restrain the center of mass of the water slab, but
*

*> given its size, the surface of the water is still probably able to
*

*> move around a little with moderate distortion of the slab. So for a
*

*> given value of the reaction coordinate, the surface can move back and
*

*> forth and adapt to the ion's position. This probably makes the process
*

*> harder to sample, because you have to sample large fluctuations of the
*

*> whole slab instead of small local fluctuations of the interface. That
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*> could probably be diagnosed with a detailed inspection of the
*

*> trajectory in VMD.
*

*>
*

*> Of course, there is no simple coordinate to describe the actual
*

*> distance of the ion to the water interface. Still, if you follow JC's
*

*> advice and use a smaller slab, the precision of your RC will improve.
*

*>
*

*> Best,
*

*> Jerome
*

*>
*

*>
*

*> On 4 May 2012 15:51, JC Gumbart<gumbart_at_ks.uiuc.edu> wrote:
*

*>> Yes. But I still question the need for such a large slab to look at just
*

*>> one ion.
*

*>>
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*>>
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*>>
*

*>> From: Xiaohu Li [mailto:xiaohu-li_at_northwestern.edu]
*

*>> Sent: Friday, May 04, 2012 8:49 AM
*

*>> To: JC Gumbart
*

*>> Cc: namd-l_at_ks.uiuc.edu List
*

*>> Subject: Re: namd-l: forces saved in forcedcd
*

*>>
*

*>>
*

*>>
*

*>> Thanks, JC.
*

*>>
*

*>> I recall that ABF also uses the colvar subroutine, which means that it is
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*>> also un-parallelized?
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*>>
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*>>
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*>>
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*>> Xiaohu
*

*>>
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*>>
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*>>
*

*>> On May 4, 2012, at 12:58 AM, JC Gumbart wrote:
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*>>
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*>>
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*>>
*

*>> My gut feeling is that the separate restraints are contaminating your PMF.
*

*>> Why do you need such a large slab?
*

*>>
*

*>>
*

*>>
*

*>> The ABF tutorial gives an example of what you're trying to
*

*>> do: http://www.ks.uiuc.edu/Training/Tutorials/namd/ABF/tutorial-abf.pdf
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*>>
*

*>>
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*>>
*

*>> See if you can reproduce those results and then modify things one at a time
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*>> from there to determine where the potential error is appearing.
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*>>
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*>>
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*>>
*

*>> On May 3, 2012, at 10:40 PM, Xiaohu Li wrote:
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*>>
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*>>
*

*>>
*

*>> I first tried to use the colvar option to apply a harmonic constraint
*

*>> between the center of mass of the liquid slab and the ion, however, since my
*

*>> slab has tens of thousands of atoms, the un-parallelized colvar code slow
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*>> down my
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*>>
*

*>> simulation by a factor of ten!
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*>>
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*>> So instead, I applied a very large harmonic constraint on the COM of the
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*>> slab using the SMD option and another harmonic constraint on the ion using
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*>> regular harmonic constraint.
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*>>
*

*>> Of course, the slab has been equilibrated.
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*>>
*

*>> Another thing is that when I inserted my ion into the slab, I used VMD to
*

*>> deleted A solvent molecule nearby to avoid any close contact. I'm guessing
*

*>> this effect is small since I have like 700 solvent molecules.
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*>>
*

*>> I ran each window dynamics for 600ps, where the first 100ps was discarded as
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*>> equilibration.
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*>>
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*>>
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*>>
*

*>> Xiaohu
*

*>>
*

*>>
*

*>>
*

*>> On May 3, 2012, at 10:05 PM, JC Gumbart wrote:
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*>>
*

*>>
*

*>>
*

*>> It's easier to set up, but should be equivalent in the end.
*

*>>
*

*>>
*

*>>
*

*>> How did you prepare and run your US sims? I cannot for the life of me
*

*>> figure out why you are getting an oscillatory pattern from US.
*

*>>
*

*>>
*

*>>
*

*>> On May 3, 2012, at 9:57 PM, Xiaohu Li wrote:
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*>>
*

*>>
*

*>>
*

*>> I have used umbrella sampling by either using WHAM or averaging the forces
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*>> the the window.
*

*>>
*

*>> How's ABF compared to those approaches? Are there any qualitative
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*>> differences?
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*>>
*

*>>
*

*>>
*

*>> Xiaohu
*

*>>
*

*>>
*

*>>
*

*>> On May 3, 2012, at 8:11 PM, JC Gumbart wrote:
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*>>
*

*>>
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*>>
*

*>> How are you calculating the PMF? Did you try, say, ABF?
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*>>
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*>>
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*>>
*

*>> On May 3, 2012, at 7:51 PM, Xiaohu Li wrote:
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*>>
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*>>
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*>>
*

*>> Hi, Chris,
*

*>>
*

*>> Thanks for taking time for pondering on my question.
*

*>>
*

*>> In my case, I would have to stick with the NVT simulation since I'm
*

*>> using the drude polarizable force field. The reason I ask is because I'm
*

*>> doing a PMF of ions pulled out of bulk(glycerol), which the reaction
*

*>> coordinates is quite simple as the surface normal direction. I'm seeing
*

*>> something quite difficult to explain since from a very naive understanding,
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*>> the PMF should be flat deep in the bulk(as seen in water, methanol, etc...).
*

*>> I'm getting quite oscillatory pattern in the bulk and the i'm talking about
*

*>> several kcal/mol oscillation(using either wham or the direct forces). That
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*>> leads me to this question. Something I notice is that the frequency of the
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*>> Langevin friction affect the self-diffusion. So extrapolate from that, it
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*>> should affect the forces.
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*>>
*

*>> Any more opinions on that?
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*>>
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*>>
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*>>
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*>>
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*>>
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*>> Xiaohu
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*>>
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*>>
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*>>
*

*>> On May 3, 2012, at 6:42 PM, Chris Harrison wrote:
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*>>
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*>>
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*>>
*

*>> Yes. However, in the limit of converged sampling the Langevin forces are
*

*>> theoretically canceling out to noise. ...theoretically. In practice, it is
*

*>> entirely possible that when using a Langevin thermostat you might see the
*

*>> periodicity produced from the kicks when analyzing the forces.
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*>>
*

*>>
*

*>> "Will the Langevin forces affect PMF calculations?" That entirely depends
*

*>> on the PMF you are performing. Many considerations go into answering that
*

*>> question. Consider: Are the forces being predominately measured in the PMF
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*>> of a small enough scale that the Langevin kicks can be resolved? If
*

*>> performed correctly, the Langevin forces should look like noise. Another
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*>> consideration: a purist would argue to perform an NVE simulation, removing
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*>> as many external forces/perturbations from the system as possible.
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*>>
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*>>
*

*>>
*

*>> Unfortunately the answer to your question is: yes, they can affect PMFs, but
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*>> a) will it matter for the question you are asking, and b) you will have to
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*>> test to actually determine for sure; or alternatively pursue an NVE ensemble
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*>> simulation.
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*>>
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*>>
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*>>
*

*>> Best,
*

*>>
*

*>> Chris
*

*>>
*

*>>
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*>>
*

*>>
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*>>
*

*>>
*

*>>
*

*>> On Thu, May 3, 2012 at 3:43 PM, Xiaohu Li<xiaohu-li_at_northwestern.edu>
*

*>> wrote:
*

*>>
*

*>> Dear NAMD users,
*

*>> I have a question regarding the forces saved in forcedcd file.
*

*>> suppose I'm doing NVT using Langevin dynamics, will the forces saved in
*

*>> forcedcd contain the random forces from Langevin dynamics?
*

*>> Do those random forces affect, say, PMF calculations if they are
*

*>> included?
*

*>> Thanks.
*

*>>
*

*>>
*

*>>
*

*>>
*

*>>
*

*>> --
*

*>>
*

*>> Chris Harrison, Ph.D.
*

*>>
*

*>> NIH Center for Macromolecular Modeling and Bioinformatics
*

*>>
*

*>> Theoretical and Computational Biophysics Group
*

*>> Beckman Institute for Advanced Science and Technology
*

*>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
*

*>>
*

*>> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
*

*>>
*

*>> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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*>>
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*>>
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*>>
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**Next message:**Hall McDull: "A question about the CHARMM force field"**Previous message:**Aron Broom: "Re: Umbrella sampling-reliability of results"**In reply to:**Jérôme Hénin: "Re: forces saved in forcedcd"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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