From: Xiaohu Li (xiaohu-li_at_northwestern.edu)
Date: Fri May 04 2012 - 10:31:41 CDT
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
> 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.
>>
>>
>>
>> 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
>> also un-parallelized?
>>
>>
>>
>> Xiaohu
>>
>>
>>
>> On May 4, 2012, at 12:58 AM, JC Gumbart wrote:
>>
>>
>>
>> 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
>>
>>
>>
>> See if you can reproduce those results and then modify things one at a time
>> from there to determine where the potential error is appearing.
>>
>>
>>
>> On May 3, 2012, at 10:40 PM, Xiaohu Li wrote:
>>
>>
>>
>> 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
>> down my
>>
>> simulation by a factor of ten!
>>
>> So instead, I applied a very large harmonic constraint on the COM of the
>> slab using the SMD option and another harmonic constraint on the ion using
>> regular harmonic constraint.
>>
>> Of course, the slab has been equilibrated.
>>
>> 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.
>>
>> I ran each window dynamics for 600ps, where the first 100ps was discarded as
>> equilibration.
>>
>>
>>
>> Xiaohu
>>
>>
>>
>> On May 3, 2012, at 10:05 PM, JC Gumbart wrote:
>>
>>
>>
>> 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:
>>
>>
>>
>> I have used umbrella sampling by either using WHAM or averaging the forces
>> the the window.
>>
>> How's ABF compared to those approaches? Are there any qualitative
>> differences?
>>
>>
>>
>> Xiaohu
>>
>>
>>
>> On May 3, 2012, at 8:11 PM, JC Gumbart wrote:
>>
>>
>>
>> How are you calculating the PMF? Did you try, say, ABF?
>>
>>
>>
>> On May 3, 2012, at 7:51 PM, Xiaohu Li wrote:
>>
>>
>>
>> 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,
>> 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
>> leads me to this question. Something I notice is that the frequency of the
>> Langevin friction affect the self-diffusion. So extrapolate from that, it
>> should affect the forces.
>>
>> Any more opinions on that?
>>
>>
>>
>>
>>
>> Xiaohu
>>
>>
>>
>> On May 3, 2012, at 6:42 PM, Chris Harrison wrote:
>>
>>
>>
>> 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.
>>
>>
>> "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
>> of a small enough scale that the Langevin kicks can be resolved? If
>> performed correctly, the Langevin forces should look like noise. Another
>> consideration: a purist would argue to perform an NVE simulation, removing
>> as many external forces/perturbations from the system as possible.
>>
>>
>>
>> Unfortunately the answer to your question is: yes, they can affect PMFs, but
>> a) will it matter for the question you are asking, and b) you will have to
>> test to actually determine for sure; or alternatively pursue an NVE ensemble
>> simulation.
>>
>>
>>
>> Best,
>>
>> Chris
>>
>>
>>
>>
>>
>>
>>
>> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:30 CST