Justin, thanks for advises.
Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). James 2012/10/3, Justin Lemkul <jalem...@vt.edu>: > > > On 10/3/12 8:59 AM, James Starlight wrote: >> 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 >> > > I don't know if that will have much of an effect or not. The values in > vdwradii.dat are used to determine if there is atomic overlap with > coordinates > being added (solvent) to the solute configuration. > > -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