Thanks for your clue. I found the very interesting paper about that force field.
Thanks again, lina ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Thomas Piggot [t.pig...@soton.ac.uk] Sent: Friday, October 01, 2010 9:22 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol I can think of a few cholesterol topologies just off the top of my head: GROMOS43A1-S3 forcefield has an entry for cholesterol There is a stream file for cholesterol available for use with the CHARMM forcefields. There are other available too, you should use google to find them. I have never used any of them so would not like to comment on which to use, this is up to you to decide after a thorough read of the literature. Cheers Tom #ZHAO LINA# wrote: > Hi, > > Thanks for your answer, I will spend some time to figure it out. > > By the way, any links or literature or something relevant to it warmly > welcome to introduce them to me. > > Best regards, > > lina > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Justin A. Lemkul [jalem...@vt.edu] > Sent: Friday, October 01, 2010 9:06 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] cholesterol > > #ZHAO LINA# wrote: >> Hi, >> >> It will be so bad for me if it really does not exist. >> I wish probably except asking Dr. google, someone else will be able to >> provide me some links. >> I once just wanted to see some examples how they handled its topology even I >> got one from >> PRODRG server, but it has problems later. Not so much in those specific >> simulations yet, just beginning stage. >> > > If your problem is with deriving parameters, then do a thorough literature > search. Simulations with cholesterol have been done with numerous force > fields, > so parameterization methodology and/or suitable parameters should be > available. > > -Justin > >> lina >> >> ________________________________________ >> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on >> behalf of Justin A. Lemkul [jalem...@vt.edu] >> Sent: Friday, October 01, 2010 8:35 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] cholesterol >> >> #ZHAO LINA# wrote: >>> Hi, >>> >>> Are there some tutorials handling the cholesterol stuff. I read several >>> literature but choked in some places. >>> >> I said this to someone just the other day: if it's not linked at >> http://www.gromacs.org/Documentation/Tutorials or you can't find it with >> Google, >> it probably doesn't exist. >> >> What's more, "handling the cholesterol stuff" doesn't really lend itself to >> getting useful help. What are you trying to do? Derive parameters? Build a >> membrane? A micelle? An LDL complex? >> >> -Justin >> >>> Thanks with best regards, >>> >>> lina >>> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> 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://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists