[gmx-users] PMF of large protein

Matteus Lindgren matteus.lindgren at chem.umu.se
Wed Feb 17 12:47:37 CET 2010

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?  


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 Lindgren, graduate student
Department of Chemistry, Umeå University 
SE-901 87 Umeå, Sweden
Phone:  +46 (0)90-7865368  



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