Dear all! Recently I've forced with the same problem as was in this topic :)
I have tieleman's lipids consisted of 128 dppc with water. also I have system with the protein inserted in the same bilayer I wounder to know 1- How I could change lipid number in the pure lipid bilayer ( increase up to 200 lipids) with standard Gromacs tools ? I've tried use genbox -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 where 8.045 in x and y was higher than in the case of initial bilayer ( 6.045) As the consequence that prodyce larger system with increased amount of water in upper and lower layers but the lipid number was the same. 2- Is there any way to increase lipid number ( to add lipids from each size of the system) in the bilayer with the inserted protein ? Thanks for help, James 2012/6/11, Justin A. Lemkul <jalem...@vt.edu>: > > > On 6/11/12 6:05 AM, James Starlight wrote: >> Dear all! >> >> >> Recently I've forced with the opposite problem. I have pre-equilbrated >> bilayer >> of highter dimensions than I need. How I could reduce lipid number of >> such >> bilayer as well as reduce total dimensions of such system ? >> >> E.g I have preequilibrated bilayer consisted of 340 lipids. I want to >> reduce it >> to the 200 lipids by the symmetrical deletion of the unnecessary lipids >> from >> each side. Is there simplest way to do it ? >> > > Try genbox with the -box option (with your bilayer as -cs) to set a smaller > box > size that will give a suitable number of lipids. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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
