<br><br><div class="gmail_quote">On Thu, May 3, 2012 at 5:17 PM, Weingarth, M.H. <span dir="ltr"><<a href="mailto:M.H.Weingarth@uu.nl" target="_blank">M.H.Weingarth@uu.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hello,<br>
<br>
I am a bit confused by a comment which I find in all MARTINI example md.mdp scripts concerning the tc-groups :<br>
<br>
It is stated there to couple groups separately:<br>
<br>
<< MARTINI -Normal temperature and pressure coupling schemes can be used. It<br>
; is recommended to couple individual groups in your system seperately>><br>
<br>
I am simulating a mixed dppc:dppg membrane (see below my parameters). Even these two different lipids-types should be coupled separately? (and how about Na+ (Qd particles) and water - also separately?)<br>
<br>
I would greatly appreciate any comment on this issue.<br>
<br>
Thanks a lot<br>
Markus<br>
<br>
<br>
<br>
<span style="font-style:italic">my parameter:</span><br style="font-style:italic">
<span style="font-style:italic">; Temperature coupling:</span><br style="font-style:italic">
<span style="font-style:italic">tcoupl = berendsen</span><br style="font-style:italic">
<span style="font-style:italic">; Groups to couple separately:</span><br style="font-style:italic">
<span style="font-style:italic">tc-grps = DPPC DPPG W NAA Protein</span><br>
<br></div></div></blockquote><div><br></div><div>Generally in membrane protein simulations different coupling groups are used to increase the accuracy of the calculations (more realistic). In your system you can make make three groups: Protein, Lipids(DPPC+DPPG) and Sol+Ions(Na+Qd)</div>
<div> </div><div><br></div><div>-Anirban</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="direction:ltr;font-size:10pt;font-family:Tahoma">
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<br>
</div>
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<br>--<br>
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