Justin,<br><br>Could you tell me for what purposes the definition of the several ref_t values could be usefull? Does this just for measurements of the temperature during simulation for each group separately or is there something else?<br>
<br><br>By the way as I've found in literature another important question about such simulation in high temperature conditions is the selection of the integrator algorithm wich also could enhanse sampling under this conditions.š E.g I've found that the BD integrator could be more usefull than leap-frog MD. What timestep and other importnat options defined in mdp should be tken into account within simulation with BD ? I've never perform simulations with this integrator and could not realise how it could enhanse simulation rate in comparison to the MD and what artifacts should expect from that :)<br>
<br><br>James<br><br><div class="gmail_quote">9 ÁĐŇĹĚŃ 2012šÇ. 22:31 ĐĎĚŘÚĎ×ÁÔĹĚŘ Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> ÎÁĐÉÓÁĚ:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Mark,<br>
<br>
<br>
<br>
<br>
<br>
š šAssuming you're raising your temperature during equilibration and<br>
š šthen running at high temperature, then you don't want water moving<br>
š šinto the receptor interior during equilibration for the same reason<br>
š šyou didn't want water moving into the CCl4. And you're going to run<br>
š šfurther equilibration after taking off all the restraints anyway,<br>
š šright? And if water moves into the receptor interior, then it<br>
š šprobably does that under high-temperature equilibrium conditions...<br>
<br>
<br>
It is that I want to prevent movement of water into Ccl4 layer (that is drive by the increased temperature and have not been present in the natural conditions) but allow it to move into the receptor interiour ( that is normally observed experimentally). So the posres application may prevent water to move both into the receptor and Ccl4 so this aproach could not be useful in my case, couldn't it ?<br>
<br>
š<br>
</blockquote>
<br></div>
No, it wouldn't. šI don't understand why you believe some water absolutely can't leak into the CCl4 layer, at least transiently. šIf you're getting massive mixing, then that's a problem for which I don't know a clear solution in this case. šOccasional leakage is not unexpected, as it even occurs in lipid bilayers. šTrue, water and CCl4 are not particularly miscible, but to say that they should remain 100% isolated in reality is not correct.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
š šOn point, the reference temperature has little to do with whether<br>
š šphases diffuse into (or out of) each other, and lots to do with what<br>
š šensemble you might be sampling. The actual temperature controls the<br>
š šrate of such diffusion, of course, but if the non-bonded<br>
š šinteractions allow for intermixing, then you'll get some degree of<br>
š šthat regardless of any other setting. You'd be well advised to check<br>
š šthat your CCl4-water boundary behaves acceptably before you invest<br>
š šin the protein simulation...<br>
<br>
<br>
Specifically I've desided to rise temperature of my system to increase conformation sampling of the protein surrounded of the interiour. For this I've devided my system on several parts to couple to separate thermostates. One part is the protein and CCl4 layer wich mimick the membrane and another part is the sorrounded water ( SOL), internal water ( wich may present in the protein interiour transitory but never in the Ccl4 layer) and IONS ( wich are always in the SOL layer). In order that increase the rate of conformation sampling I've gradually increased ref_t of each t_group. In part this result in evaporation of water and some of that water has moved in Ccl4 layer. So its intresting for me might šI set ref_t for water_ions group as the specified value ( ref_t= 310 k) and gradually increase only ref_t for the protein_ccl4 group in the annealing manner. As the consequence I want to prevent evaporation of the water but maintain of the overal temperature high of my system tp increase sampling of the protein conformation ?<br>
<br>
I inderstand that such aproach is very unphysical but aplication of the posres and other tricks are from this theme but works good in some cases :)<br>
<br>
<br>
</blockquote>
<br></div>
This sounds really fishy to me. šCoupling different parts of a system to thermostats at different temperatures just begs for artifacts. šThe use of thermostats for separate parts of the system, even at the same temperature, is questionable since you violate energy conservation. šOf course, for many cases, they're a necessity and we just go ahead with it ;) šIf you've got two parts of a system in thermal disequilibrium, then you've got a very odd system with thermostats exchanging different amounts of energy with different portions of the system. šI don't know how to predict the effects of such a setup, but I don't recall having seen anything like this done before.<div class="im HOEnZb">
<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br></div><div class="HOEnZb"><div class="h5">
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