Justin,thanks! <br><br><br>1) For example for the situation presented in manual for 2 groups with 3 and 4 points the time enty should be<br><br><a name="sa"><tt>annealing_time = 0 3 6 0 2 4 6<br><br></tt></a>from this I've understood that 0 value is the start of timer for each group and subsequent values are the actual time in the ps, havennt it ?<br>
<br>For example I'd like to perform nvt simulation ( with overal time 100ps) for three different groups in 5 equal steps. So does annealing options must be <br><br><tt><a name="sa"><tt>annealing = single single single</tt></a></tt><br>
<tt><a name="sa"><tt>annealing_npoints = 5 5 5</tt></a></tt><br><tt><a name="sa"><tt>annealing_time = 0 25 50 75 100 0 25 50 75 100 0 25 50 75 100<br><br></tt></a></tt><a name="sa"><tt>annealing_temp = 300 310 320 330 340 350</tt></a><a name="sa"> </a><a name="sa"><tt>300 310 320 330 340 350</tt></a><a name="sa"> </a><a name="sa"><tt>300 310 320 330 340 350</tt></a><a name="sa"><br>
# this means that for each group temperature increase on 10K on each step and there are 5 steps for each grou ( equal to npoints)<br></a><a name="sa"></a><a name="sa"></a><tt><a name="sa"><tt><br>Does this ecxample correct or there are some connection between that values for diffent groups ?<br>
</tt></a></tt><br>2) How I can couple this annealing options with the <b>gen_temp</b> values wich as I understood must also differs on the each step ? OR should I use some averaged gen_temp?<br><br>James<br><br><br><div class="gmail_quote">
4 апреля 2012 г. 16:05 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">
<div class="im"><br>
<br></div>
It can be done in one .mdp file with the simulated annealing feature.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Finally what exactly is tau_t time constant?<br>
<br>
</blockquote>
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See manual section 3.4.8.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
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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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