<pre><br></pre><pre>&gt;At&nbsp;2010-10-18&nbsp;12:56:31，chris.neale@utoronto.ca&nbsp;wrote:

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

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

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

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

&gt;

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

&gt;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;simulation&nbsp;&nbsp;

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

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

&gt;

&gt;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;

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

&gt;

&gt;Chris.

&gt;</pre><pre><p class="MsoNormal" style="text-indent:10.5pt;mso-char-indent-count:1.0"></p><p class="MsoNormal" style="text-indent:10.5pt;mso-char-indent-count:1.0"><span lang="EN-US">Hi, Chris! Thanks for the reply! I have not conducted unfolding

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

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

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

1257-1282').<o:p></o:p></span></p><p class="MsoNormal" style="text-indent:10.5pt;mso-char-indent-count:1.0"><span lang="EN-US"><span style="mso-spacerun:yes">&nbsp;</span>I've searched the maillist

and noticed some issues about High temperature simulations. I'm not sure

whether the 'ilmm' force field has been optimized for high temperature

simulation. I also noticed some users asked about MD parameters in 'unfolding a

protein'. And the parameters they used are different from ours' (e.g. the

'rlist', 'rcoulomb' and 'temperature or pressure couple algorithm').<o:p></o:p></span></p><p class="MsoNormal" style="text-indent:10.5pt;mso-char-indent-count:1.0"><span lang="EN-US"><span style="mso-spacerun:yes">&nbsp;</span>I just want to make sure I

didn't make mistakes in these parameters which maybe cause the protein keeping

in a compact state! The radius of gyration of the protein fluctuated around

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

parameters I chose have no problem, then I could keep going. Any comment?</span></p><p class="MsoNormal" style="text-indent:10.5pt;mso-char-indent-count:1.0"><span lang="EN-US"><br></span></p></pre><pre>&gt;Hi,

&gt;If I can add to this discussion, I think that your results are very 

&gt;reasonable. Proteins in solution are not straight lines, but fold to 

&gt;some extent. If you wish to have en elongated protein you have to pull 

&gt;it like it is being done in AFM experiments.

&gt;

&gt;Itamar</pre><pre><p class="MsoNormal" style="text-indent:10.5pt;mso-char-indent-count:1.0"><span lang="EN-US">Hi, Itamar! Thanks for the reply! I didn't intend to make the

unfolding protein like a straight line. I just 'feel' the protein in 498K

should fluctuate a little larger. So I want to make sure I didn't make mistake

in MD parameters setting or water BOX preparing.</span></p></pre><pre>

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

&gt;

&gt;Hi&nbsp;All,

&gt;

&gt;I&nbsp;met&nbsp;a&nbsp;problem&nbsp;when&nbsp;I&nbsp;try&nbsp;to&nbsp;unfold&nbsp;a&nbsp;protein&nbsp;using&nbsp;Gromacs,&nbsp;It&nbsp;&nbsp;

&gt;seemed&nbsp;the&nbsp;protein&nbsp;cannot&nbsp;be&nbsp;totally&nbsp;unfolded!

&gt;

&gt;The&nbsp;simulated&nbsp;system&nbsp;has&nbsp;one&nbsp;Engrailed&nbsp;Homeodomain&nbsp;(En)&nbsp;protein&nbsp;(a&nbsp;&nbsp;

&gt;three&nbsp;helix&nbsp;bundle&nbsp;protein&nbsp;with&nbsp;54&nbsp;residues,&nbsp;629&nbsp;atoms),&nbsp;total&nbsp;4848&nbsp;&nbsp;

&gt;spce&nbsp;waters,&nbsp;and&nbsp;7&nbsp;Cl-&nbsp;used&nbsp;to&nbsp;neutralize&nbsp;the&nbsp;system&nbsp;in&nbsp;a&nbsp;5.752(nm)^3&nbsp;&nbsp;

&gt;water&nbsp;BOX.&nbsp;I&nbsp;use&nbsp;the&nbsp;NTP&nbsp;ensemble&nbsp;with&nbsp;T=498K&nbsp;and&nbsp;P=26atm.&nbsp;The&nbsp;system&nbsp;&nbsp;

&gt;has&nbsp;1nm&nbsp;thick&nbsp;water&nbsp;in&nbsp;each&nbsp;side&nbsp;of&nbsp;the&nbsp;En&nbsp;protein,&nbsp;and&nbsp;the&nbsp;density&nbsp;of&nbsp;&nbsp;

&gt;the&nbsp;system&nbsp;has&nbsp;been&nbsp;adjusted&nbsp;to0.829&nbsp;g/cm3.

&gt;

&gt;The&nbsp;simulation&nbsp;lasted&nbsp;24ns.&nbsp;The&nbsp;helixes&nbsp;disappeared&nbsp;at&nbsp;about&nbsp;4ns.&nbsp;And&nbsp;&nbsp;

&gt;after&nbsp;that&nbsp;some&nbsp;beta&nbsp;sheet&nbsp;formed&nbsp;in&nbsp;the&nbsp;N&nbsp;terminal&nbsp;of&nbsp;the&nbsp;protein.&nbsp;&nbsp;

&gt;However,&nbsp;the&nbsp;protein&nbsp;kept&nbsp;in&nbsp;a&nbsp;compact&nbsp;state&nbsp;during&nbsp;the&nbsp;24ns&nbsp;&nbsp;

&gt;simulation.&nbsp;The&nbsp;radius&nbsp;of&nbsp;gyration&nbsp;of&nbsp;the&nbsp;protein&nbsp;fluctuated&nbsp;around&nbsp;&nbsp;

&gt;1.1nm&nbsp;during&nbsp;the&nbsp;simulation.

&gt;

&gt;I've&nbsp;also&nbsp;noticed&nbsp;similar&nbsp;simulation&nbsp;done&nbsp;by&nbsp;others.&nbsp;For&nbsp;example,&nbsp;&nbsp;

&gt;David&nbsp;Becka&nbsp;and&nbsp;Valerie&nbsp;Daggett&nbsp;reviewed&nbsp;their&nbsp;En&nbsp;protein&nbsp;unfolding&nbsp;in&nbsp;&nbsp;

&gt;paper&nbsp;"Methods&nbsp;for&nbsp;molecular&nbsp;dynamics&nbsp;simulations&nbsp;of&nbsp;protein&nbsp;&nbsp;

&gt;folding/unfolding&nbsp;in&nbsp;solution.&nbsp;Methods&nbsp;34&nbsp;(2004)&nbsp;112¨C120".&nbsp;The&nbsp;&nbsp;

&gt;simulations&nbsp;were&nbsp;performed&nbsp;with&nbsp;ENCAD&nbsp;and&nbsp;ilmm,&nbsp;and&nbsp;used&nbsp;an&nbsp;0.8nm&nbsp;&nbsp;

&gt;cutoff&nbsp;range.&nbsp;And&nbsp;the&nbsp;ensemble&nbsp;they&nbsp;used&nbsp;is&nbsp;NVE&nbsp;as&nbsp;I&nbsp;know.&nbsp;A&nbsp;stretched&nbsp;&nbsp;

&gt;unfolding&nbsp;state&nbsp;occurred&nbsp;at&nbsp;about&nbsp;5ns&nbsp;in&nbsp;their&nbsp;60ns&nbsp;simulation&nbsp;in&nbsp;&nbsp;

&gt;498K,&nbsp;with&nbsp;little&nbsp;helix&nbsp;structure.

&gt;

&gt;I&nbsp;was&nbsp;wondering&nbsp;whether&nbsp;the&nbsp;difference&nbsp;is&nbsp;caused&nbsp;by&nbsp;using&nbsp;different&nbsp;MD&nbsp;&nbsp;

&gt;software&nbsp;and&nbsp;force&nbsp;field,&nbsp;or&nbsp;by&nbsp;some&nbsp;wrong&nbsp;parameters&nbsp;in&nbsp;my&nbsp;.mdp&nbsp;file.&nbsp;&nbsp;

&gt;I've&nbsp;also&nbsp;conducted&nbsp;another&nbsp;18ns&nbsp;simulation,&nbsp;and&nbsp;the&nbsp;result&nbsp;is&nbsp;almost&nbsp;&nbsp;

&gt;the&nbsp;same.&nbsp;I&nbsp;list&nbsp;he&nbsp;mdp&nbsp;file&nbsp;below.&nbsp;Any&nbsp;comment&nbsp;is&nbsp;appreciated!

&gt;

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