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