Date: Fri Jul 20 2012 - 04:44:48 CDT
>> If you apply this restraint, it will not change the manner in which you generate the PMF, that is, you will still only use your reaction coordinate forces and harmonic centers as input to WHAM with the data for the reaction coordinate trajectory over that window.
I know that people actually do the WHAM in this manner but in principle you just need the total bias energy whixh is in the restraint potential in most cases but not necessarily. Think for instance in the case when you do this with temperature, then you do a 2D histogram of potential energy and reaction coordinate. In the same fashion i can add the umbrella energy plus the base restraint energy to have the total bias energy of the microstate and then histogram those energies and my original reaction coordinate.
Anyhow, i just decided to extend the DNA a couple of bases to not interfere with my calculation. As we are trying to model DNA binding to a promoter the opening is physically unrealistic since this is a side effect of truncating the DNA. Bases DO open when they are in the end, but the DNA should not end up there in the first place.
Regarding a 2d with the H-bond, it is not an option since this calculation already requires close to a microsecond and the second dimention seems to be very irrelevant for the process.
----Mensaje original---- De: broomsday_at_gmail.com Fecha: 18-jul-2012 9:47 Para: "felmerino_at_uchile.cl"<felmerino_at_uchile.cl> CC: <namd-l_at_ks.uiuc.edu> Asunto: Re: namd-l: Umbrella Sampling plus restraints Hi Felipe,If you apply this restraint, it will not change the manner in which you generate the PMF, that is, you will still only use your reaction coordinate forces and harmonic centers as input to WHAM with the data for the reaction coordinate trajectory over that window. This doesn't mean, however, that your restraint might not change the PMF. The "real" PMF (at least as far as the forcefield is concerned), is the one where there are no extra restraints, but, that assumes that you have sampled long enough to get good coverage of all the relevant microstates. So in your case with the base opening, the particular windows of the reaction coordinate in which you see this happening might need to be sampled for longer. One problem I would say about your wanting to add the restraint is, what reason do you have for believing the base DOESN'T open up? Do you trust (to a reasonable extent) the forcefield parameters for the DNA? If so, then the base must be opening up because there is a more favourable interaction with the protein, and restraining it may give a false result on the PMF where your binding appears weaker, or the activation energy higher, than it really is. Something you might try is 2D Umbrella sampling, in which the second reaction coordinate is a distance or H-bonding or something for that base-pair, then you could see if the lowest free energy path for separation of your DNA-protein complex involves a movement of that base. If you don't have a good reason for believing that base is entirely non-dynamic, then I would suggest you might have found a rather interesting "gate-keeping" element on your reaction path. Anyway, something I would highly recommend is to use MetaDynamics initially to look at this. It is far easier to setup than Umbrella Sampling, requires less manual intervention (deciding on new force constants and centers) and generally give a good rough idea of the PMF much faster, not to mention that extending it to 2D (2 reaction coordinates) is trivial, whereas Umbrella Sampling in 2D can be taxing. You can then use that metadynamics bias in a static way and perform Umbrella Sampling on top of it in order to refine the PMF and get error bars. ~Aron
On Wed, Jul 18, 2012 at 8:18 AM, felmerino_at_uchile.cl <felmerino_at_uchile.cl> wrote:
We are working currently in some free energy calculations on a protein DNA complex using unbrella sampling with the minimal distance between the two molecules as the rea_ction coordinate. Everything goes OK except that the last base pair in the DNA opens from time to time and contacts the protein. We would like to restrain it in order to maintain the watson-crick pairing but we don't know if it would do any harm to the PMF. As we are using tcl forces we know exactly how much energy the bias is applying to the system so in principle the should be no mixing between the pulling restraint and the bais pairing restraint.
We were then wondering if somebody can point to anything against this approach. Also, i am not sure now if we need to use only the bias energy for the unbrella restraint or it is better to add the ones from the bases restraint in order to do the histograming as well. In principle, i think you need to add all the extra energy added to obtain every particular microstate, but i am not sure.
-- Aron Broom M.ScPhD StudentDepartment of ChemistryUniversity of Waterloo
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