> > > Stefan Hoorman wrote: > > > I am starting again my calculations for the real system and this am > > going to use as starting positions distances in intervals of 0.1nm. Some > > of them aren't really 0.1nm apart since the distance between the > > twogroups in my first trajectory does not always increase in a steady > > way, but the average distance between them is close enough to 0.1nm. I > > looked back in the mailing list and found something about applying > > restraints to these simulation windows. I imagine these restraints refer > > to the umbrella potential still on and not actual restraining as in > > adding -DPOSRES, right? > > Without a link to the post you're reading, I can't comment on that. It > probably > refers to the umbrella biasing (restraining) force, but without context, > that's > just a guess. > > > One other thing I've noticed is that the distance between my groups > > decrease in several of my windows, as one would expect since the two > > structures still interact with each other, and in some cases they get > > back to the original distance prior to the separation. Is this normal > > for the WHAM analysis? > > I don't understand what you mean. There should be some fluctuation about a > mean > position in each window. The umbrella potential maintains this distance, > on > average, if you're doing things right. > > Justin >
Ok, here is what I meant. I use each of the starting position extracted from my original pulling trajectory (i mean the trajectory with "pull_rate = 0.01") to simulate each window. Each of these windows still have the umbrella force constant (pull_k1 = 35) but now have "pull_rate = 0". My system, though, does not fluctuate about a mean position in each window. My system returns to the initial dimer or tries to if the distance is too big and the simulation time not long enough. So, whem I analyse the distance between the two groups with g_dist in each of the sampling windows, I get a series of decreasing values that will eventually return to the 0.9 nm. For these simulations, I keep the same parameters as in the original pull trajectory. The vectors are still the same, the force constant is still the same. I only change the "pull_rate" from 0.01 to 0 and "pull_geometry" from direction to distance (because g_wham asks tells me "pull_geometry = direction" is not supported). So maybe I am doing something wrong.
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