Justin,<br><br><br>I have not quite sure about methodology of aplication of such harmonic distance restrains yet.<br><br>E.g I want to constraint distancec of the backbone atoms of my protein within 7 A ( to allow deviation of all backnones up to 7 A)<br>
<br>I've tried <br><br>genrestr -f start.gro -n index.ndx -disre -disre_dist 0.7 -disre_frac 0.7 -disre_up2 1.0<br><br>From this I've obtained for first 5 backbone atoms below disres<br><br> 1 5 1 0 1 0.0441928 0.250426 1.25043 1<br>
1 10 1 1 1 0.0697795 0.395417 1.39542 1<br> 1 12 1 2 1 0.101657 0.576059 1.57606 1<br> 1 14 1 3 1 0.138237 0.783341 1.78334 1<br>
1 15 1 4 1 0.160509 0.909554 1.90955 1<br><br>so the atoms 1 and 5 would be unconstrained if the distance between them would be 0.004-0.25, atoms 1 and 10 would be constrained within distance 0.069-0.395 etc.<br>
<br>I'm not quite understood from manual if the disre_dist exactly that range value ralative atom coordinate in the start.gro ? What is the -desre_frac and in what cases in could be usefull ?<br><br><br>James<br><br>
<div class="gmail_quote">10 มะาลฬั 2012ว. 18:25 ะฯฬฺุฯืมิลฬุ Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> ฮมะษำมฬ:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
<div class="im"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
So I suppose that the presence of the some constrained factor is needed to prevent destabilisation but allow conformation sampling. I see three alternative ways of my production MD run with enhanced sampling.<br>
<br>
1- First of all as the most trivial way I'm thinking of using soft posres applied on backbone atoms only with the constained value ( 50-100 kj*nm2) corresponded to the energy of the thermal motion.<br>
<br>
2- Also I've thought about application of the harmonic distance_restraince (instead of posres) on the all backbone atoms exept of flexible loops where this disres must be in the longer range ( e.g up to 15-20A) but I could not realise about usefullness of such aproach because I cant define value for such disres for the atoms in helixes. <br>
</blockquote>
<br></div>
Sure you can. Use genrestr with a suitable index group. The use of lots of distance restraints precludes the use of DD, so you're limited to using mdrun -pd, which is a lot slower and may counteract any perceived benefit in terms of simulation time.<div class="im">
<br>
</div></blockquote></div><br>