Dear Gramacs, Anybody know where I can get "Dowser" for water in channel?
Thanks a lot! [gmx-users] water in channel Eric Jakobsson jake at ncsa.uiuc.edu Mon Jan 19 22:50:02 CET 2004 Previous message: [gmx-users] water in channel Next message: [gmx-users] water in channel Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Approach # 2) will not work for all channels. We published a paper in Biophys. J. a number of years ago in which we looked at water motion in the gramicidin channel with the protein immobile but the water at 300 K. The water moved locally in the normal way, but had no motion along the channel at all. I am sure if we had started with the channel empty and the gramicidin frozen, it would never have filled, at least not in any reasonable time. On the other hand, for some channels if you don't immobilize them and you don't have contents in the lumen, the lumenal structure will become unstable. So approach # 1) (Dowser or some equivalent method) is the better way, based on our group's experience. Eric At 11:31 AM 1/19/2004 -0500, you wrote: >I can think of 2 options: > >1) There is a program called "Dowser" put out by J. Hermans' lab at >UNC-Chapel hill. It usually works very well. > >2) You can position restrain the channel and allow water and bilayer to >move freely during MD. It should not take long for water to enter the >channel ... that is, providing that it is actually supposed to do so. Water >is probably the fastest diffusing species in your system. You can take >advantage of this. > >David > >-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >David Bostick Office: 262 Venable Hall >Dept. of Physics and Astronomy Phone: (919)962-0165 >Program in Molecular and Cellular Biophysics >UNC-Chapel Hill >CB #3255 Phillips Hall dbostick at physics.unc.edu >Chapel Hill, NC 27599 http://www.unc.edu/~dbostick >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > >On Mon, 19 Jan 2004, Itamar Kass wrote: > > > Hi all, I am currently working on a channel in a DMPC bilayer (and > water). After inserting the channel into the bilayer (using Graham's > modified mdrun) I am facing a new problem. I want to put water in the > channel and did not succeed in doing it. Using pr simulation I did not > succeed, then I tried to use genbox, but it puts water in the membrane also. > > Does someone have an idea or face it and has a solution? > > Thank you, Itamar. > > > > ******************************************** > > Computers are like airconditioners... They don't work well with Windows > open. > > ******************************************** > > > > =========================================== > > | Itamar Kass > > | The Alexander Silberman > > | Institute of Life Sciences > > | Department of Biological Chemistry > > | The Hebrew University, Givat-Ram > > | Jerusalem, 91904, Israel > > | Tel: +972-(0)2-6585146 > > | Fax: +972-(0)2-6584329 > > | Email: ikass at cc.huji.ac.il > > | Homepage: > http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html > > ============================================ > >_______________________________________________ >gmx-users mailing list >gmx-users at gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-request at gromacs.org. --------------------------------- Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 4021 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 fax 217-244-2909 (Currently on leave to the National Institutes of Health in Bethesda, Maryland, to be Director of the NIGMS Center for Bioinformatics and Computational Biology and Chair of the NIH Biomedical Information Science and Technology Initiative Consortium, but maintaining my research lab at Illinois by periodic commuting. My usual schedule is four days a week at NIH and three days a week at Illinois.) ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ _______________________________________________ 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