<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>The separation of groups for temperature control is originally necessary to avoid (or correct for) temperature gradient in the system, which occurs when systems parts have different frequencies of motions. Typically the water molecules and a protein would be separated to avoid the freezing of the protein and the heating up of the solvent.</div><div><br></div>It would not make much difference to couple the dppc and dppg lipid groups separately or together. To form a separate group you need a sufficient amount of particle to avoid large (and therefore more difficult to control) fluctuations. Ions are generally coupled to the solvent they are embedded into.<div><br></div><div>Anirban suggestion is fine.</div><div><br></div><div><div>On May 3, 2012, at 1:56 PM, Anirban Ghosh wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><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"> <div> <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"> <br> <br> </div> </div> <br>--<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br> Please don't post (un)subscribe requests to the list. Use the<br> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br> -- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br></body></html>