From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Jan 31 2011 - 16:39:37 CST
Hi guys,
Try the colvars (collective variables) module of NAMD 2.7: you can
define a colvar as a difference of two RMSD values. Then you can apply
a moving restraint to that variable, or even run metadynamics.
Cheers,
Jerome
On 31 January 2011 22:53, V.Ovchinnikov <ovchinnv_at_mit.edu> wrote:
> You are right about the compilation issue. However, I also have a
> version of TMD that I used in a TCL script (for which you obviously need
> just the binary); this was a somewhat painful exercise that I undertook
> in 2006 because the official NAMD 2.6 version of TMD had a bug which was
> visible only in parallel runs, (apparently, I wasn't clever enough to
> fix the source code & recompile). The bug was fixed a couple of years
> ago.
>
> ( If you are wondering, the consuming part in tcl was coding the
> best-fit rotation a la Kabsch 76, which involves diagonalization )
>
> So, while you figure out how to compile the source, I can also send to
> you the TCL script (it is not slow if the number of forced atoms is
> small, e.g. if you run an explicit water simulation and apply the
> restraint to the protein atoms only)
>
> Will be in touch,
> Victor
>
> On Mon, 2011-01-31 at 15:33 -0600, Minh, David D. wrote:
>> Dear Victor,
>>
>> Thanks for the fast reply!
>>
>> Yes, it would be quite helpful to see your code. Please send it when you find the time. If there is interest in the community, I could help polish this code for later inclusion.
>>
>> I still need a way to compile the source code on my Mac, though. I've only worked with the binaries before. Hopefully somebody else knows what I can do about that problem.
>>
>> Thanks!
>> David
>>
>> On Jan 31, 2011, at 3:14 PM, V.Ovchinnikov wrote:
>>
>> > Dear David,
>> >
>> > I have tinkered with the restrained version of TMD that is in NAMD2.6 a
>> > couple of years ago, and I think I have a version that performs a
>> > double-sided TMD using two orientation structures, as you describe
>> > (although I was not using it to compute work, just to look possible
>> > paths). If you give me a couple of days to dig up the relevant files, I
>> > can send them to you off-the-list. Not quite sure how the TMD 2.7 source
>> > code is different from TMD 2.6, but I would be surprised if the
>> > differences were large. (One could polish the code and submit to the
>> > developers for inclusion later, too, if the community thinks its
>> > useful.)
>> >
>> > Regards,
>> > Victor
>> >
>> >
>> > On Mon, 2011-01-31 at 13:12 -0600, Minh, David D. wrote:
>> >> A minor change to targeted MD can make it possible to calculate
>> >> potentials of mean force in the region between two structures.
>> >>
>> >>
>> >> Right now, the code allows targeting toward one final structure, with
>> >> the potential given by the following equation,
>> >> U_{TMD} = \frac{1}{2} \frac{k}{N} [ RMS(t) - RMS^*(t) ]^2
>> >> http://www.ks.uiuc.edu/Research/namd/2.7/ug/node41.html
>> >>
>> >>
>> >> It should be relatively easy to modify targeted MD and have the option
>> >> of targeting the transition between two structures. The potential
>> >> would be,
>> >> U_{TMD} = \frac{1}{2} \frac{k}{N} [ DRMS(t) - DRMS^*(t) ]^2,
>> >> with DRMS(t) = RMS_1(t) - RMS_2(t), and RMS_1 being the RMSD from
>> >> structure 1 and RMS_2 being the RMSD from structure 2, and DRMS^*(t)
>> >> being a time-dependent function. This bias was used in,
>> >> NK Banavali and B Roux. Free Energy Landscape of A-DNA to B-DNA
>> >> Conversion in Aqueous Solution. J. Am. Chem. Soc. 127(18), 6966-6876
>> >> (2005).
>> >> K Arora and CL Brooks. Large-scale allosteric conformational
>> >> transitions of adenylate kinase appear to involve a population-shift
>> >> mechanism. PNAS 104(47), 18496-18501 (2007).
>> >> and probably other papers.
>> >>
>> >>
>> >> Using the theory described in,
>> >> G Hummer and A Szabo. Free energy reconstruction from nonequilibrium
>> >> single-molecule pulling experiments. PNAS 98(7), 3658-61 (2001).
>> >> one could calculate the PMF along the DRMS coordinate from a set of
>> >> TMD trajectories. The theory described in,
>> >> DDL Minh. Multidimensional Potentials of Mean Force from Biased
>> >> Experiments along a Single Coordinate. J. Phys. Chem. B 111,
>> >> 4137-4140 (2007).
>> >> can be used to calculate the PMF along other coordinates, or 2D PMFs.
>> >> The theory in,
>> >> DDL Minh and AB Adib. Optimized Free Energies from Bidirectional
>> >> Single-Molecule Force Spectroscopy. Phys. Rev. Lett 100(18), 180602
>> >> (2008).
>> >> DDL Minh and JD Chodera. Optimal estimators and asymptotic variances
>> >> for nonequilibrium path-ensemble averages. J. Chem. Phys. 131(13),
>> >> 134110 (2009).
>> >> would be useful for combining data for the transition from structure 1
>> >> to structure 2 and the reverse process from structure 2 to structure
>> >> 1.
>> >>
>> >>
>> >> Actually, it is possible to reconstruct PMFs with the current TMD
>> >> code, but I think the PMF between two structures would be more
>> >> interesting.
>> >>
>> >>
>> >> I'd like to give this a try. Would any NAMD developers be interested
>> >> in making this modification? Any thoughts?
>> >
>>
>
>
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