Matteus Lindgren wrote:
Dear all,
I will try to calculate PMF with gromacs for the first time and I have
some basic questions regarding this.
I will calculate the PMF of moving a relatively large protein (700
residues) through water a distance of 2nm towards a perfectly flat TiO2
surface in order to estimate the interaction between the protein and the
surface and the effect of modifications of the mineral surface. The
total system is around 120 000 atoms and I can run about 4ns per day. My
first question is simply: is it practically possible to run a number of
PMF calculations of the protein movement for such a large system?
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?
If you're referring to the tutorial linked from the Gromacs site, please note
that those distances were found to be acceptable for that particular system, and
may not be generalizable to all systems. Further, 1 ns of sampling in each
window probably isn't enough for very large systems.
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?
Constraint pulling can be used for SMD (generating a series of initial
configurations) or for calculation of PMF, although not with WHAM. There was a
post about this a day or two ago; see the archives.
-Justin
Thank you
Matteus
---------------------------------------------------------
Matteus Lindgren, graduate student
Department of Chemistry, Umeå University
SE-901 87 Umeå, Sweden
Phone: +46 (0)90-7865368
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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