Or it could be a PBC issue, that sections of chain that appear to be dangling out into space actually enter the other side of the box.
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Justin A. Lemkul > Sent: Thursday, 10 February 2011 4:26 AM > To: ra...@fis.unam.mx; Discussion list for GROMACS users > Subject: Re: [gmx-users] Dangling phospholipids > > > > Dr. Ramón Garduño-Juárez wrote: > > Dear All, > > > > First of all I want to tank Justin Lemkul and Thomas Piggot for their > > useful comments that helped me to resolve my previous questions > > regarding the construction of a lipid membrane. > > > > Now I would like to post this question to this forum. > > > > I got through placing a putative ion channel into a DPPC bilayer. I > > managed to expand this sytem -> minimize it -> shrink it (several > times) > > -> minimize it (several times) until I got an adequate lipid density. > > > > After viewing the final results I noticed that there are several > lipid > > molecules that are dangling at the end of the periodic box. > > > > Is this normal, or I did something wrong?. If this is expected, How > do I > > get rid of the dangling lipid molecules before I start a MD > simulation? > > > > By "dangling" do you mean that they are somewhat isolated from the rest > of the > lipids? If so, how many are there? Usually this just indicates that > you're not > done shrinking the membrane back to appropriate dimensions. The final > box > vectors achieved through shrinking should usually be fairly close to > the > original dimensions of the system. If this is not the case, then > you're not > done building your system. > > -Justin > > > Waiting for your replies... > > > > Sincerely, > > Ramon Garduno > > > > -- > ======================================== > > 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 -- 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
