<div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Stefan Hoorman wrote:<br>
<br>
> I am starting again my calculations for the real system and this am<br>
> going to use as starting positions distances in intervals of 0.1nm. Some<br>
> of them aren't really 0.1nm apart since the distance between the<br>
> twogroups in my first trajectory does not always increase in a steady<br>
> way, but the average distance between them is close enough to 0.1nm. I<br>
> looked back in the mailing list and found something about applying<br>
> restraints to these simulation windows. I imagine these restraints refer<br>
> to the umbrella potential still on and not actual restraining as in<br>
> adding -DPOSRES, right?<br>
<br>
Without a link to the post you're reading, I can't comment on that. It probably<br>
refers to the umbrella biasing (restraining) force, but without context, that's<br>
just a guess.<br>
<br>
> One other thing I've noticed is that the distance between my groups<br>
> decrease in several of my windows, as one would expect since the two<br>
> structures still interact with each other, and in some cases they get<br>
> back to the original distance prior to the separation. Is this normal<br>
> for the WHAM analysis?<br>
<br>
I don't understand what you mean. There should be some fluctuation about a mean<br>
position in each window. The umbrella potential maintains this distance, on<br>
average, if you're doing things right.<br>
<br>Justin<br></blockquote></div><br>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.<br>
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).<br>
So maybe I am doing something wrong.<br>