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? Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Tuesday, August 21, 2012 3:09 PM Subject: Re: [gmx-users] EM in kalp15_DPPC On 8/21/12 6:35 AM, Shima Arasteh wrote: > Allright, I will check the configurations of out and inputs to find out the > reason of warning. > Please let me know something: > Should I expect to see changes in area per lipids in each shrinking or it > would happen after 25th repeat suddenly? > It will decrease steadily. Make sure your loop is calling the correct coordinate file each time. The energy-minimized output of the previous step is the input into the next iterations of shrinking, i.e.: system_inflated.gro -> em_inflated.gro em_inflated.gro -> system_shrink1.gro -> em_shrink1.gro em_shrink1.gro -> system_shrink2.gro -> em_shrink2.gro etc. -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
