By the way I've completed equilibration phase of my system ( receptor in Ccl4-water membrane mimicking layer) in the hight temperature conditions. :)<br><br>During 3ns I gradually increased temperature from 300 to 700k with posres applied on the Ccl4 C atoms and all atoms of protein. After this I've changed posres applied on the protein to the backbone atoms only and started gradually decrease fc falue ( from 1000 to 250 ). The overal system was stabile and I've noticed linnear increase of the total energy accompanied by such increase of temperature.<br>
<br>Thanš When I've removed posres from side-chains I've noticed bigger RMSD in potential energy of my system.<br><br>The only artifact that I've noticed is that some water was moved into the Ccl4 layer during this equilibration. How I could prevent such layer mixing without applying posres on water? I need free-water in my system because I want to see how some water move into the receptor that have a chanell wich some internal- water cavities having functional meaning.<br>
Does some operation with the COM option could prevent mixing of some differen solvent layers ?<br>At the curent moment I've difined COM as<br><br>Protein_CCl4 SOL_NA_CL_XW<br><br>where XW is the water observed in the X-ray structure of that protein ( I've defined that mollecules in separate layer)<br>
<br>Thanks for help<br><br>James<br><br><br><div class="gmail_quote">4 ÁÐÒÅÌÑ 2012šÇ. 18:14 ÐÏÌØÚÏ×ÁÔÅÌØ Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> ÎÁÐÉÓÁÌ:<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">
Justin,<br>
<br>
<br>
1) I've defined 5 steps for specified definition of the time of each step as well as for more flexibile controle of the such annealing: e.g I want that equilibration step corresponded to the temperature between 320 and 330K will be longer than between first step corresponded to 300-310K etc<br>
<br>
</blockquote>
<br></div>
OK, that makes sense. šWhat you showed before does not do that, hence my confusion.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
2) About velosities. As I understood for annealing equilibration gen_temp must be equal to the starting temperature of such equilibration ( gen_temp= 300 in the above example). But in what exactly circumstances the changing in gen_temp could be usefull? As I've told after such annealing equilibration I want to simulate my system on the high temperature condition for efficient conformation sampling. Might it be that initial high velocities could be usefull for such sampling efficacy?<br>
<br>
</blockquote>
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I'm not clear on what you're asking. šIf you are generating velocities (which you wouldn't after you reach your target via SA or equilibration), then you don't need gen_temp or gen_vel. šIf you're starting a new run, then gen_temp should be equal to the ref_t value you wish to use for the simulation. šIf your gen_temp and ref_t values are not the same, then it is quite possible that the simulation will crash or give very unexpected results due to potential instabilities in the thermostat algorithm.<div class="HOEnZb">
<div class="h5"><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>
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