Justin, Might the modifications of the vdwradii.dat be suitable for such system expanding or (on other hand) reduction (as in the below picture are shown). In the lattter case I defined new box dimensions (smaller than initial box dims) and would like to remove all side water-lipids layer which are beyond new pbc dimensions)?
http://imageshack.us/content_round.php?page=done&l=img138/5497/reduction.png James 2012/10/3, Justin Lemkul <jalem...@vt.edu>: > > > On 10/3/12 1:59 AM, James Starlight wrote: >> Justin, >> >> I've told about lower lipid density at the left and right edges of the >> new system ( see new pic bellow with marked regions). >> >> http://imageshack.us/photo/my-images/10/dppc.png/ >> >> I've started with system consisted of 118 lipids and 6000 water in dims >> 6x6x10 >> >> I've created new box with the desired sizes for my system as well as >> centered it in it. Finally I've resized it via >> genbox -cp prot_in_lipids_old.gro -cs dppc128_whole.gro -box 8.04542 >> 8.04542 10.19156 >> >> >> As the result I've obtain syste of 128 lipids and 13000 water with dims >> 8x8x10 >> >> I have the same system with the popc lipids with the same dims where >> there are 200 lipids >> >> Why only 10 lipids were added after resizing ? How I could increase >> this number of added lipids ( expesially in regions with lower lipid >> density- see pic) ? >> > > genbox decides whether or not to put molecules in the box if they can be > added > intact; anything sticking out of the box is removed. Since water molecules > are > small, this is easy to do. Since a lipid molecule is large, it is not so > easy. > The hydrocarbon tails are very flexible and thus may have configurations > leading them to stick out of the box, so genbox won't add them. You will > likely > have to gradually increase the box dimensions in x and y to allow for more > lipids to be added, striking a balance between the (much larger) number of > water > molecules and number of lipids added. > > -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
