<p class="MsoNormal" style="text-indent:10.5pt;mso-char-indent-count:1.0"><span lang="EN-US">This information is helpful! </span></p>

<p class="MsoNormal" style="text-indent:10.5pt;mso-char-indent-count:1.0"><span lang="EN-US">I think I need to deal with the simulation result really carefully.

Thanks for the help! And also thanks Massimo for the information about expected

gyration radius of a purely non-interacting random chain!</span></p><div><div></div><pre><span class="Apple-style-span" style="white-space: normal;"><br></span>At&nbsp;2010-10-18&nbsp;21:01:23，chris.neale@utoronto.ca&nbsp;wrote:

&gt;Chen,

&gt;

&gt;to&nbsp;answer&nbsp;this,&nbsp;please&nbsp;see&nbsp;David's&nbsp;post&nbsp;and&nbsp;my&nbsp;reply.&nbsp;To&nbsp;answer&nbsp;if&nbsp;&nbsp;

&gt;your&nbsp;unfolded&nbsp;state&nbsp;ensemble&nbsp;is&nbsp;accurate,&nbsp;you&nbsp;will&nbsp;need&nbsp;to&nbsp;know&nbsp;some&nbsp;&nbsp;

&gt;experimentally&nbsp;evaluated&nbsp;quantities&nbsp;of&nbsp;the&nbsp;state&nbsp;that&nbsp;you&nbsp;are&nbsp;trying&nbsp;&nbsp;

&gt;to&nbsp;reproduce:&nbsp;498K,&nbsp;26&nbsp;atm,&nbsp;a&nbsp;certain&nbsp;amount&nbsp;of&nbsp;salt,&nbsp;etc,&nbsp;(but&nbsp;not&nbsp;&nbsp;

&gt;including&nbsp;the&nbsp;forcefield&nbsp;model&nbsp;or&nbsp;cutoffs,&nbsp;which&nbsp;are&nbsp;obviously&nbsp;&nbsp;

&gt;intrinsically&nbsp;part&nbsp;of&nbsp;the&nbsp;model).

&gt;

&gt;Then,&nbsp;if&nbsp;your&nbsp;data&nbsp;does&nbsp;not&nbsp;match&nbsp;this,&nbsp;then&nbsp;you&nbsp;can&nbsp;conclude&nbsp;that&nbsp;the&nbsp;&nbsp;

&gt;simulation&nbsp;time&nbsp;was&nbsp;too&nbsp;short&nbsp;or&nbsp;the&nbsp;parameters&nbsp;were&nbsp;not&nbsp;valid.&nbsp;Also,&nbsp;&nbsp;

&gt;I&nbsp;guarantee&nbsp;it&nbsp;was...&nbsp;you'll&nbsp;probably&nbsp;need&nbsp;something&nbsp;more&nbsp;like&nbsp;10&nbsp;ms&nbsp;-&nbsp;&nbsp;

&gt;10&nbsp;s&nbsp;(what&nbsp;is&nbsp;the&nbsp;unfolding&nbsp;rate&nbsp;under&nbsp;these&nbsp;conditions?),&nbsp;which&nbsp;is&nbsp;&nbsp;

&gt;rather&nbsp;difficult&nbsp;to&nbsp;obtain).

&gt;

&gt;Comparing&nbsp;a&nbsp;temperature&nbsp;denatured&nbsp;state&nbsp;to&nbsp;an&nbsp;AFM&nbsp;denatured&nbsp;state,&nbsp;one&nbsp;&nbsp;

&gt;does&nbsp;not&nbsp;expect&nbsp;them&nbsp;to&nbsp;match.&nbsp;The&nbsp;point&nbsp;here&nbsp;was&nbsp;to&nbsp;ask:&nbsp;are&nbsp;you&nbsp;sure&nbsp;&nbsp;

&gt;that&nbsp;your&nbsp;ensemble&nbsp;of&nbsp;conformations&nbsp;is&nbsp;incorrect&nbsp;given&nbsp;the&nbsp;conditions?

&gt;

&gt;Chris.

&gt;

&gt;--&nbsp;original&nbsp;message&nbsp;--

&gt;

&gt;&gt;&nbsp;At&nbsp;2010-10-18&nbsp;12:56:31£¬chris.neale&nbsp;at&nbsp;utoronto.ca&nbsp;wrote:

&gt;&gt;&nbsp;Generally,&nbsp;forcefields&nbsp;are&nbsp;not&nbsp;parameterized&nbsp;for&nbsp;temperatures&nbsp;other&nbsp;&nbsp;&nbsp;

&gt;&gt;&nbsp;than&nbsp;298K,&nbsp;so&nbsp;simulations&nbsp;are&nbsp;not&nbsp;expected&nbsp;to&nbsp;reproduce&nbsp;the&nbsp;expected&nbsp;&nbsp;

&gt;&gt;&nbsp;&nbsp;properties&nbsp;(like&nbsp;boiling&nbsp;water&nbsp;and&nbsp;the&nbsp;correct&nbsp;temperature&nbsp;&nbsp;&nbsp;

&gt;&gt;&nbsp;denaturation&nbsp;of&nbsp;proteins).

&gt;&gt;

&gt;&gt;&nbsp;There's&nbsp;almost&nbsp;certainly&nbsp;other&nbsp;issues&nbsp;here&nbsp;(including&nbsp;the&nbsp;fact&nbsp;that&nbsp;&nbsp;&nbsp;

&gt;&gt;&nbsp;I'm&nbsp;entirely&nbsp;sure&nbsp;that&nbsp;you&nbsp;can&nbsp;get&nbsp;a&nbsp;lot&nbsp;more&nbsp;than&nbsp;24&nbsp;ns&nbsp;of&nbsp;&nbsp;

&gt;&gt;&nbsp;simulation&nbsp;&nbsp;on&nbsp;a&nbsp;54&nbsp;aa&nbsp;protein;&nbsp;and&nbsp;26&nbsp;atom&nbsp;of&nbsp;pressure&nbsp;seems&nbsp;pretty&nbsp;&nbsp;

&gt;&gt;&nbsp;arbitrary)&nbsp;&nbsp;but&nbsp;it&nbsp;will&nbsp;come&nbsp;down&nbsp;to&nbsp;this&nbsp;eventually.

&gt;&gt;

&gt;&gt;&nbsp;Just&nbsp;because&nbsp;you&nbsp;found&nbsp;a&nbsp;paper&nbsp;in&nbsp;which&nbsp;they&nbsp;get&nbsp;a&nbsp;denatured&nbsp;state&nbsp;&nbsp;&nbsp;

&gt;&gt;&nbsp;does&nbsp;not&nbsp;imply&nbsp;that&nbsp;they&nbsp;got&nbsp;the&nbsp;correct&nbsp;denatured&nbsp;state.

&gt;&gt;

&gt;&gt;&nbsp;Chris.

&gt;&gt;

&gt;

&gt;Hi,&nbsp;Chris!&nbsp;Thanks&nbsp;for&nbsp;the&nbsp;reply!&nbsp;I&nbsp;have&nbsp;not&nbsp;conducted&nbsp;unfolding

&gt;before,&nbsp;so&nbsp;I&nbsp;compared&nbsp;my&nbsp;result&nbsp;with&nbsp;other's&nbsp;to&nbsp;make&nbsp;sure&nbsp;it&nbsp;is&nbsp;reasonable&nbsp;in

&gt;some&nbsp;extend.&nbsp;The&nbsp;26&nbsp;atm&nbsp;pressure&nbsp;comes&nbsp;from&nbsp;experiment&nbsp;result&nbsp;(Haar&nbsp;et&nbsp;al.,

&gt;1984)&nbsp;mentioned&nbsp;in&nbsp;some&nbsp;MD&nbsp;related&nbsp;papers&nbsp;(e.g.&nbsp;'J.&nbsp;Mol.&nbsp;Biol.&nbsp;(2000)&nbsp;296,

&gt;1257-1282').

&gt;

&gt;&nbsp;&nbsp;I've&nbsp;searched&nbsp;the&nbsp;maillist

&gt;and&nbsp;noticed&nbsp;some&nbsp;issues&nbsp;about&nbsp;High&nbsp;temperature&nbsp;simulations.&nbsp;I'm&nbsp;not&nbsp;sure

&gt;whether&nbsp;the&nbsp;'ilmm'&nbsp;force&nbsp;field&nbsp;has&nbsp;been&nbsp;optimized&nbsp;for&nbsp;high&nbsp;temperature

&gt;simulation.&nbsp;I&nbsp;also&nbsp;noticed&nbsp;some&nbsp;users&nbsp;asked&nbsp;about&nbsp;MD&nbsp;parameters&nbsp;in&nbsp;&nbsp;

&gt;'unfolding&nbsp;a

&gt;protein'.&nbsp;And&nbsp;the&nbsp;parameters&nbsp;they&nbsp;used&nbsp;are&nbsp;different&nbsp;from&nbsp;ours'&nbsp;(e.g.&nbsp;the

&gt;'rlist',&nbsp;'rcoulomb'&nbsp;and&nbsp;'temperature&nbsp;or&nbsp;pressure&nbsp;couple&nbsp;algorithm').

&gt;

&gt;&nbsp;&nbsp;I&nbsp;just&nbsp;want&nbsp;to&nbsp;make&nbsp;sure&nbsp;I

&gt;didn't&nbsp;make&nbsp;mistakes&nbsp;in&nbsp;these&nbsp;parameters&nbsp;which&nbsp;maybe&nbsp;cause&nbsp;the&nbsp;protein&nbsp;keeping

&gt;in&nbsp;a&nbsp;compact&nbsp;state!&nbsp;The&nbsp;radius&nbsp;of&nbsp;gyration&nbsp;of&nbsp;the&nbsp;protein&nbsp;fluctuated&nbsp;around

&gt;1.1nm&nbsp;(never&nbsp;bigger&nbsp;than&nbsp;1.4nm)&nbsp;during&nbsp;our&nbsp;30ns&nbsp;simulation&nbsp;now.&nbsp;If&nbsp;the&nbsp;MD

&gt;parameters&nbsp;I&nbsp;chose&nbsp;have&nbsp;no&nbsp;problem,&nbsp;then&nbsp;I&nbsp;could&nbsp;keep&nbsp;going.&nbsp;Any&nbsp;comment?

&gt;

&gt;

&gt;

&gt;--

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