Justin,<br><br><br><div class="gmail_quote">10 апреля 2012 г. 16:21 пользователь Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> написал:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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I have never used the bd integrator so I cannot offer any help here. I don't see any magical reason why you should expect it to enhance sampling though.</blockquote><div><br> I've found in the literature that this integrator could rise the integration-time-step from common 1-2fs used with the MD-integrator.<br>
<br><br><br>By the way I've tried to test my system equilibrated in the hight temperature in different conditions. As the consequence when I've removed all posres ( on the last stage of equilibration it's value was 200 for backbone atoms only) from my protein the alpha helixes have been destabilised already after 3ns of such unconstrained simulation ( ref_t= 700k).<br>
<br>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. It's known that conformation transitions wich I want to ssample accompanied by the large scale motions in the helical segments ( up to 10-15 A). At the same time such big fluctuations on the other atoms may destabiise regions wich are more rigid. Should I define several sets of restrains for my protein to allow one regions move with bigger amplitudes in comparison with rigid fragments ? <br>
<br>3- Finally alternative aproach is the ussage of common temperature ( ref_t=310k) in the production run but using starting velocities obtained from the nvt equilibrration obtained with the hight ( 700k) temperature. Can I enhance sampling using that starting conditions ?<br>
<br><br>What from this three strategies is the most suitable? IS there any alternative ways for such high-temperature simulation ?<br><br><br>Thanks for help again,<br><br><br>James<br></div></div>