Hi; i'm doing umbrella sampling.i did pulling of AA from surface and then different conformation with trjconv and then umbrella sampling.....i thought that 0.9 nm was the closest distance from surface because when i changed the pullratejust for 0.001 nm/ns the run crashed, so ithought it couldn't be closer more.so i run md for umbrella then gmx wham. but when i check and draw the profile.xvg file, energy had min value in 0.6 nm! and was repulsive in closer distances. i didn't sample any closer distance from 0.9 nm and didn't md_umbrella run for it because i didn't see closer distances in summary distances.datfile(token fro gmx distance).How could be possible?i didn't know it before. Then i modified the dt to half of its former value and increased nsteps 2times so there is not any change in simulation time,BUT at this time i got the closer distances(in comparison with 0.9 nm), 0.5 nm! HOW can i be sure that dt=X is the best value and my AA will not be closer more even i change the simulation time or pullrate or anything else? Before these happenings i thought that when the run doesn't crush everything is OK, but now i don't have any idea! could you please help me?
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