From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri May 04 2012 - 08:51:43 CDT
Yes. But I still question the need for such a large slab to look at just
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
I recall that ABF also uses the colvar subroutine, which means that it is
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:
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
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
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
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:
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?
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
On Thu, May 3, 2012 at 3:43 PM, Xiaohu Li <xiaohu-li_at_northwestern.edu>
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
-- 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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