According to tutorials, sampling at every 0.1nm is sufficient so 20
points*sampling time ~1 ns = 20ns which could be ok but then there is
not time to allow for much protein rotation. Opinions about this?
I think it is difficult to estimate how quickly such a PMF converges,
but probably extremely slowly. You would have to sample over all
rotations of the protein which would rather take microseconds (or
longer) than nanoseconds. The question is, how exact should the PMF be.
Plusminus 1kcal (no chance to get there, I guess), or plusminus 5 kcal
(difficult?), or 10 kcal (possible?)? The only way to find out is to
try. You can do the complete umbrella sampling twice with *really
independent* starting frames (e.g. different protein orientations) and
check the difference between the PMFs.
Cheers,
Jcohen
My second question concerns the pull code. I understand how to use the
umbrella sampling and g_wham to calculate PMF but how is constraint
pulling used? Pros and cons?
Thank you
Matteus
---------------------------------------------------------
Matteus Lindgren, graduate student
Department of Chemistry, Umeå University
SE-901 87 Umeå, Sweden
Phone: +46 (0)90-7865368
--
---------------------------------------------------
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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