<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;">
<br>
Stefan Hoorman wrote:<br>
><br>
><br>
> > The distances between the two structures in each of the windows<br>
> are (in nm):<br>
> > 0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 =<br>
> 1.52; 2500<br>
> > = 1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000<br>
> = 1.7;<br>
> > 5250 = 1.62; 5500 = 1.6; 5750 = 1.73; 6000 = 1.85; 6250 = 1.86;<br>
> 6500 =<br>
> > 1.91; 6750 = 1.84; 7000 = 1.88; 7250 = 1.82; 7500 = 1.93 ; 7750 =<br>
> 2.04;<br>
> > 8000 = 2.16 ; 8250 = 2.3 ; 8500 = 2.32 ; 8750 = 2.45 ; 9000 = 2.52 ;<br>
> > 9250 = 2.5 ; 9500 = 2.62 ; 9750 = 2.65 ; 10000 = 2.66<br>
><br>
> There is substantial overlap and jumping back and forth (i.e., 1.56,<br>
> decrease to<br>
> 1.54, increase to 1.56, then back to 1.52, etc) in these distances,<br>
> so I think<br>
> they are not optimal for umbrella sampling. Instead of more regular<br>
> spacing in<br>
> time, I would suggest more regular spacing in terms of distance. Most<br>
> literature on the topic cites how far apart windows were in terms of<br>
> distance,<br>
> which is important for WHAM analysis.<br>
><br>
> -Justin<br>
><br>
><br>
> Is there a way to do this automatically in gromacs? To extract<br>
> structures from the simulation based on the distance between them?<br>
><br>
><br>
<br>
No, but you can use a script that iteratively calls g_dist on separate<br>
structures from your trajectory (trjconv -sep). See, for example:<br>
<br>
<a href="http://oldwiki.gromacs.org/index.php/Making_Commands_Non-Interactive" target="_blank">http://oldwiki.gromacs.org/index.php/Making_Commands_Non-Interactive</a><br>
<br>
-Justin<br>
<br>
<br></blockquote><div>I have a test set which is comprised of the same constituents of my real system, except the solvent (i mean, it is in vacuum. This test set I use to (as the name says) test different different parameters without having to wait too much. I know it would not serve as a very quantitative set, but even though, when I changed the force_constant of the umbrella potentia to a lower value (from 35 to 10) I got something out of the WHAM that looked more like a "rollercoaster", I little bit edgy perhaps, but at least not a downstream line like the one before. When I changed it again to 5 kJ, the graphic still looked like a rollercoaster but it differed in 1 or 2 kcal more negative than the one with 10 kJ as umbrella force constant. Perhaps, in addition to space my intervals as a function of distance, my spring constant is wrong. Does that make any sense?<br>
Ahh...by the way, the link for oldwiki is not working. I will try it later.<br><br></div></div><br>