<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>
> I have performed a series of umbrella sampling simulations in order to<br>
> do a WHAM analysis. The profile.xvg file I obtain is a continuous<br>
> descending line along my distance axis. There is no increase in energy<br>
> after my two structures separate. Perhaps I am doing something wrong.<br>
<br>
Sounds like it, but there's no way anyone on this list will know that unless you<br>
describe your system in greater detail - how you generated the starting<br>
configurations, how many windows you used and what distances that corresponds<br>
to, the pull parameters you've specified in your .mdp file, and anything else<br>
that might be pertinent.<br>
<br>
-Justin<br>
<br>
Ok, I've done the following. I have simulated my system (protein + ligand in water SPC with GROMOS96 53a6 forcefield, with PME, Nose-Hoover thermostat (310 K), parrinello-rahman barostat (1 atm), with the pull code for 15 ns, the pull code content of the mdp file is the following:<br>
</blockquote><div> pull = umbrella<br>pull_geometry = direction<br>pull_dim = Y Y N<br>pull_nstxout = 10<br>pull_nstfout = 1<br>pull_ngroups = 1<br>pull_group0 = protein<br>pull_group1 = SLC<br>pull_vec1 = 1 1 0<br>
pull_init1 = 0<br>pull_rate1 = 0.001<br>pull_k1 = 35<br>pull_constr_tol = 1e-06<br>pull_pbcatom0 = 0<br>pull_pbcatom1 = 0<br><br></div></div>Analysing the distance between the groups I get a very shy increase in the initial distance for the first 5 nanoseconds and after that the distance between the two groups increase 5nm in the next 10ns.<br>
>From this trajectory I have removed 30 structures. The first 10 were obtained with a 500 ps interval between them and the other 20 in 250 ps interval for the next 5ns. The final 5ns of the simulation are not of interest since my Lennard jones and coulomb interaction between the two structures fall to 0 after the first 9 ns of simulation.<br>
I then simulated each of these windows for 500 ps with the following mdp_pull content:<br><br>; Pull Code<br>pull = umbrella<br>pull_geometry = distance<br>pull_dim = Y Y N<br>pull_nstxout = 10<br>pull_nstfout = 1<br>
pull_ngroups = 1<br>pull_group0 = protein<br>pull_group1 = SLC<br>pull_vec1 = 1 1 0<br>pull_init1 = 0<br>pull_rate1 = 0<br>pull_k1 = 35<br>pull_constr_tol = 1e-06<br>pull_pbcatom0 = 0<br>pull_pbcatom1 = 0<br>
<br>I have set the "pull_geometry" to distance since g_wham does not accept "direction". <br>The distances between the two structures in each of the windows are (in nm):<br>0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 = 1.52; 2500 = 1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000 = 1.7; 5250 = 1.62; 5500 = 1.6; 5750 = 1.73; 6000 = 1.85; 6250 = 1.86; 6500 = 1.91; 6750 = 1.84; 7000 = 1.88; 7250 = 1.82; 7500 = 1.93 ; 7750 = 2.04; 8000 = 2.16 ; 8250 = 2.3 ; 8500 = 2.32 ; 8750 = 2.45 ; 9000 = 2.52 ; 9250 = 2.5 ; 9500 = 2.62 ; 9750 = 2.65 ; 10000 = 2.66<br>
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