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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear Mark,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks for contributing your ideas and suggestions, really appreciate it.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The reason I am playing with distance restraints on my protein is because I am interested to see the effects of equilibrating a protein in membrane using the
two different restraint methods i.e. distance vs. position.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Yes, without distance restraint (i.e. removing disre = simple in the mdp) will allow the simulation to run to completion very smoothly.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I will give Berendsen pressure coupling a shot and see how it goes. However, prior to applying distance restraint on my protein, I have ran 5ns of position
restraint simulation (with P-R coupling) and there weren’t any complaints/problems.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Many thanks again for your help.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Huiwen
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>Mark Abraham<br>
<b>Sent:</b> Thursday, February 23, 2012 9:48 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] Distance Restraints on Protein - possible at all?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On 22/02/2012 11:17 AM, NG HUI WEN wrote: <o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> NG HUI WEN
<br>
<b>Sent:</b> Sunday, February 19, 2012 1:19 PM<br>
<b>To:</b> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<b>Subject:</b> Distance Restraints on Protein - possible at all?</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Dear gmxusers,
</span><o:p></o:p></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> </span><o:p></o:p></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">I have been trying to apply distance restraints on my protein but have been unsuccessful thus far.</span><o:p></o:p></p>
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For what purpose?<br>
<br>
<br>
<o:p></o:p></p>
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<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> </span><o:p></o:p></p>
<p><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">I have consulted the user forum previously and with some much-appreciated help I have managed to get my simulation (with distance restraints applied) to run. However, the joy did
not last long as the simulation crashed very quickly (after ~40-50ps).</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
Do they run with no restraints?<br>
<br>
P-R P-coupling is known to be unsuitable for equilibration (see manual), so that might be a factor here.<br>
<br>
Mark<o:p></o:p></p>
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