To remove the periodicity I ran the command trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact and chose "system" . Is removing the periodicity something other than this? I don't have any idea to fix it here.:-( It is just a way to repeat the tutorial from the begining!
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Tuesday, August 21, 2012 5:00 PM Subject: Re: [gmx-users] EM in kalp15_DPPC On 8/21/12 8:01 AM, Shima Arasteh wrote: > > > Thanks for your reply. > In order to check the warning of grompp after scaling up I ran grompp again > without -maxwarn: > > grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr > WARNING 1 [file minim.mdp]: > The sum of the two largest charge group radii (3.840099) is larger than >rlist (1.200000). > > Do I need to change the minim.mdp settings? Visualizing the system doesn't > show any odd result! > Would you mind helping me? > Likely you did not correctly remove the periodicity of the DPPC membrane before inflating so you have fragmented molecules somewhere. Go back and fix it according to the instructions provided in the tutorial. -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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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
