From: Mitchell Gleed (aliigleed16_at_gmail.com)
Date: Wed Oct 08 2014 - 18:07:00 CDT
I will look into it that, thank you! That seems a reasonable solution, and
one that would still allow for the ligand to explore all psi's and phi's
over the distribution of umbrella windows. I'm still trying to grasp using
either in US-REMD, but I think I'm getting a better understanding--my
mentor and I have been debating about it a fair amount this afternoon.
I could very well be on the wrong track here so please correct me if I'm
wrong, but I've since had an idea that I could simply place the reference
atoms so their tilt is along the Z axis--perhaps simplifying things a bit
and still allowing me to use the tilt colvar. Any tilt deviation would then
be away from 0 degrees and toward 180, eliminating the need to have a sign.
Feeding the data into WHAM with this method, however, seems a bit
problematic to me. For example, if the ligand is oriented toward zero
degrees so cos(0deg)=1, then all of the colvar data will be less than 1.
Would this example and it's opposite result in extreme barriers in the PMF
at cos(theta)=1 and -1? Is this where the periodic flags are useful? I
suppose this may be the wrong forum for WHAM questions, but if anyone has
experience in that area, any suggestions would be welcome.
On Wed, Oct 8, 2014 at 2:45 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> Hello Mitchell, if the "tilt" cosine function does not work for you
> because of its symmetry, how about defining a "spinAngle" around an axis
> orthogonal to Z? That should give you the tilt angle, but with a sign (if
> I understand correctly this is what you are looking for).
> On Wed, Oct 8, 2014 at 4:38 PM, Mitchell Gleed <aliigleed16_at_gmail.com>
>> I am working on a procedure for 2D umbrella sampling of a ligand through
>> a membrane protein. The two dimensions I hope to explore are Z-distance
>> (using distanceZ from the colvars module) and tilt angle (hopefully using
>> tilt from the colvars module) of the ligand to generate a 2-D PMF.
>> I might not fully understand, but in my testing, and as explained in the
>> User Guide, the cosine of the tilt angle is measured between the atoms of
>> interest and reference atoms with 1 being parallel and -1 being
>> antiparallel to the reference atoms. However, the protein is asymmetric,
>> and a reported deviation in 10 degrees of the ligand, for example, doesn't
>> tell me whether it tilted toward +Z or -Z space, where I would expect the
>> ligand to behave differently. Furthermore, I'm not sure I could use tilt
>> with 2D-US-REMD as I've planned (based on the
>> NAMD_Source_2.10b1/replica/umbrella2d example), since replica bias centers
>> would not distinguish between +Z/-Z tilt change.
>> I'm considering post-processing the trajectories and measuring cos(theta)
>> with respect to the Z axis and then using this data to generate the PMF,
>> but disk space becomes a big issue, and it wouldn't solve the
>> replica-exchange limitation. (At which point I could switch to 1D REMD for
>> distance and employ constant tilt constraints.)
>> Can the tilt colvar be adjusted to measure the cosine of the tilt angle
>> with respect to an axis, rather than with respect to reference coordinates
>> (such as Z)? Or is there another path I could take or colvar to use to
>> study this dimension?
>> Thank you,
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
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