Re: string method in NAMD 2.10

From: Chris Chipot (
Date: Tue Sep 22 2015 - 10:26:53 CDT


you might find it useful to check out the tutorials at We have released a new
tutorial on the string method
with swarms of trajectories, which can be downloaded from there. Once
you have a converged string, the tutorial also proposes a route to compute
the free-energy change along it. Feel free to try the tutorial out and
give us
some feedback, as I am sure, it is perfectible.


Chris Chipot

On 9/22/15 8:05 AM, Jerome Karp wrote:
> Hi,
> Thanks for the helpful information! I'm surprised there doesn't seem
> to be a script included with the release - I wonder if it's there but
> I can't find it - but anyway I think this will help me get started in
> implementing the algorithm.
> Thanks again!
> - Jerry Karp
> On Tue, Sep 22, 2015 at 6:31 AM, Thomas Evangelidis <
> <>> wrote:
> ​And this:
> ​---------- Forwarded message ----------
> From: *Luca Maragliano* <
> <>>
> Date: 18 December 2014 at 15:35
> Subject: RE: string method with swarms-of-trajectories - NAMD
> implementation
> To: Thomas Evangelidis < <>>
> Hi Thomas,
> I don't know if the same code can run on GPU's, I have no
> experience on that.
> Most importantly however the code was done serially because the
> system is super-simple (the AD
> in vacuum). There is no point in doing the string method serially
> otherwise, it would be a great
> loss of time for any reasonable size system.
> The evolution is just a steepest descent in the space of CVs,
> where you use an instantaneous
> approximation of the mean force rather than the true one (which
> otherwise would be estimated
> via an average on the x at z fixed).
> the slowing down recovers for the use of instantaneous rather then
> average and it is obtained by simply
> scaling the time step of z motion wrt that of the x (which is
> internal in NAMD).
> This dynamics is performed at each image and can be sketched as
> * evolve x with NAMD + harmonic force from potential
> .5*k*(theta(x)-z)^2 and its proper tstep
> * evolve z with force k*(thetha(x)-z) and scaled tstep
> If the CV is non-linear then the mean force on z is multiplied by
> the metric factor M.
> Every few steps of this descent you reparametrize the values along
> the curve (an example code in fortran
> is also in the bundle). Reparametrization does not require MD but
> does require communication of the CV
> values of all images.
> So in general you have
> * few steps of descent in CV space, at each image independently
> of the others
> * reparametrization call
> How many steps in between rep calls depends on the system. Too few
> would require too much communication
> and too many would break the curve integrity (but you can cycle
> the reparametrization a few times, if needed).
> Again please feel free to ask at any time
> ciao,
> Luca
> ------------------------------------------------------------------------
> *From:* Thomas Evangelidis [
> <>]
> *Sent:* Thursday, December 18, 2014 2:07 PM
> *To:* Luca Maragliano
> *Subject:* Re: string method with swarms-of-trajectories - NAMD
> implementation
> Hi Luca,
> Thank you for the clarification
> For the implementation of the otf version, look at table 1 of
> our JCTC paper (page 527).
> The otf method is similar to the mean forces method except
> that steps 1-3 are
> substituted by the concurrent evolution of the CVs and the
> physical variables, coupled
> via the harmonic potential. In other words, rather than doing
> step 1 with fixed CV values
> you evolve the CVs as well but on a different, slowed-down
> time-scale, i.e. you give them
> a high mass or friction. More details are in appendix B.
> In terms of implementation, this amounts to modify the
> restraint dynamics of step 1 by
> introducing a line that evolves the CV values.
> Do those files with the "otf" keyword in their name need the
> modification you mentioned? I need to read more carefully your
> paper to understand how program the restr_dih_otf.tcl script to
> evolve the CVs slowly. Right now things are hectic, so I will
> probably come back with more questions. I just have one simple
> question, I saw you evolve the image trajectories serially. Does
> this mean the same code car run on GPUs?
> thank you for your help!
> Thomas
> ​

Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
3047 Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
405 North Mathews
Urbana, Illinois 61801                            Phone: (217) 244-5493
      It is hard for France to maintain a thirty-five-hour workweek when
      China and India have invented a thirty-five-hour workday.
                                                      Thomas L. Friedman

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