[gmx-users] g_wham PMF Profiles

ZEYNEP ABALI zabali16 at ku.edu.tr
Fri Feb 10 12:53:22 CET 2017


I appreciate your answer.

Simulation time is 200 ns per window.

Our pulling rate for the initial pulling simulation is 0.01, but the
interval between subsequent umbrella windows are 0.1 nm. When I try to add
additional windows to the region around 1.3 nm they drift away from that
position; even with a double force constant.

Also, instead of excluding these windows, if I exclude the ones with the
double peaks in the same region, then the PMF profile looks almost the same
as the one with all the windows, the more bumpy one.

Best regards,

*Zeynep ABALI*
MSc Candidate in Biomedical Sciences and Engineering
Koç University, Istanbul

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