Thanks for your invaluable reply to Justin and syma.
On Sun, 29 Jun 2008 Justin A.Lemkul wrote : > > >minnale wrote: >> >> Thanks for your prompt reply, according to you for membrane protein >> protocols keep restrain only on protein but not on lipid and water, is there >> any possibility to move water inside pore of the membrane when keep restrain >> only on protein. >>Could you please tell me >>Thanks a lot in advance >> > >Anything is possible, given the random nature of MD. It will depend largely >upon how you prepared your system. If there is a lot of void space around >your protein, then water will likely leak in over time, but may be forced out >by the hydrophobic lipid tails, if you equilibrate long enough. If your >lipids are nicely packed around your protein (using a method like InflateGRO >from Tieleman's site) then this occurrence is less likely. > >The most important thing to do is to consult the literature regarding similar >systems and take note of what those authors have done. How did they insert >the protein? How did they equilibrate the system, and for how long? > >-Justin > >> >>On Sun, 29 Jun 2008 Justin A.Lemkul wrote : >> > >> > >> >minnale wrote: >> >> >> >> HI users, >> >> I have embedded protein in popc bilayer and ran the minimisation >> >> succesfully , before going equilibration I would like to confirm one >> >> thing that how to run the equilibration with on which system keep >> >> position restrain? >> >> >> >>1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, >> >>-DPOSRES_LIPID, -DPOSRES_WATER) at a time ? >> >> >> >>or 2. keep position resrain on each system at a time and >> >> 3.is it require to keep position restrain on water? >> >>Could you tell me clearly pls >> >>Thanks alot in advance >> >> >> >> >> > >> >If you "equilibrate" your system with every element of it restrained, I >> >think you will accomplish absolutely nothing. Typical procedures for >> >membrane proteins involve equilibrating with restraints on the protein >> >only, allowing the lipids to pack around the protein. >> >-Justin >> > >> >> >> >>HSBC >> >><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL >> >> PROTECTED]/2204104_2196511/2199118/1?PARTNER=3&OAS_QUERY=null> >> >> >> >>------------------------------------------------------------------------ >> >> >> >>_______________________________________________ >> >>gmx-users mailing list gmx-users@gromacs.org >> >>http://www.gromacs.org/mailman/listinfo/gmx-users >> >>Please search the archive at http://www.gromacs.org/search before posting! >> >>Please don't post (un)subscribe requests to the list. Use the www >> >>interface or send it to [EMAIL PROTECTED] >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> >-- ======================================== >> > >> >Justin A. Lemkul >> >Graduate Research Assistant >> >Department of Biochemistry >> >Virginia Tech >> >Blacksburg, VA >> >jalemkul[at]vt.edu | (540) 231-9080 >> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> > >> >======================================== >> > >> >> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>gmx-users mailing list gmx-users@gromacs.org >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before posting! >>Please don't post (un)subscribe requests to the list. Use the www interface >>or send it to [EMAIL PROTECTED] >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >-- ======================================== > >Justin A. Lemkul >Graduate Research Assistant >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >======================================== >
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