So if it were not quite clearly :)<br><br> my main question is about methodology of such gradually temperature rise in the nvt enssemble conditions. Might it be realised by means of simple equilibation in one mdp file varying some parametries to change time-step of temperature growth? Or this methodology require several mdp files with slightly different ref_t as well as gen_temp options ? Finally what exactly is tau_t time constant?<br>
<br>James<br><br><div class="gmail_quote">3 апреля 2012 г. 13:14 пользователь James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</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">
Dear Gromacs users!<br><br><br>I want to perform simulation of the membrane protein in the Ccl4-membrane-mimicking interiour in the increaced ( up to 600 K) temperature on the nvt ensemble.<br><br>As the consequence I'd like to protect the temperature caused destabilisation of my protein and simulate native-like conformation events in the speed-up manner.<br>
<br>What should I use for preparing of my system? As I understtod I neen long nvt equilibration phase prior to productive run to addaptate my system to the uncommon conditions. For this I want to perform step-by-step increasing of the Ref_T for all separate groups of my system ( Protein_Ccl4, Water_Ions ). E.g I'll separate my equilibration phase on the 20 steps with the ref_t 310, 320, 330... 600K and the length of each step 50ps. Could this aproach could be usefull? What addition tricks could I use ( e.g dynamics of changing tau_t for different groups etc)?<br>
<br><br>Thanks for help,<br><br><br>James <br>
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