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bio-phys / PyDHAMed

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
BSD 3-Clause "New" or "Revised" License
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Generating Bias Matrix #14

Open Cal-JWRW opened 1 year ago

Cal-JWRW commented 1 year ago

I have performed an Umbrella Sampling analysis on a membrane system in gromacs. My collective variable is the distance of a small molecule from the center of a membrane. Using the pullf file generated from gromacs how would I go about generating the bias force matrix for each of my 80 US windows?

Cal-JWRW commented 1 year ago

The units of my biassing forces are kJ/mol/nm^2 at 303.15 K so which conversion should be used to get them into the required units?