I visualized the dppc128.gro and dppc128_whole.gro. The dppc seems to get smaller and more compact in dppc128_whole.gro than the dppc128.gro. I think it's normal!
Sincerely, Shima ________________________________ From: Justin Lemkul <jalem...@vt.edu> To: gmx-users@gromacs.org Sent: Tuesday, August 21, 2012 6:00 PM Subject: Re: [gmx-users] EM in kalp15_DPPC On 8/21/12 9:24 AM, Shima Arasteh wrote: > > > 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? That's the correct command. The differences between dppc128.gro and dppc128_whole.gro should be fairly apparent when visualized. > I don't have any idea to fix it here.:-( > It is just a way to repeat the tutorial from the begining! > I doubt you have to start completely over, but I know the protocol works as advertised. If molecules are still split (which is likely the case, given the error below), spotting them in the inflated system should be fairly easy with visualization. That should help you track down what's gone wrong. -Justin > > 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
