Hi Justin I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and with this settings grompp gives me two notes and one of this notes is inconsistent:
NOTE 1 [file pr.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. Because I thought rlist hast to be 1.2 and rvdw hast to be 1.2 for my CHARMM27 force field. My second note is: NOTE 2 [file pr.mdp]: The sum of the two largest charge group radii (0.079505) is larger than rlist (1.200000) - rvdw (1.200000) which I sadly don't understand. Greetings Lara ----- Ursprüngliche Message ----- Von: Justin Lemkul <jalem...@vt.edu> An: Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 17:33 Freitag, 21.September 2012 Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error On 9/21/12 11:26 AM, Lara Bunte wrote: > Hi Justin > > Sorry but I don't understand what you mean with "Despite being given the > correct settings for CHARMM27, you're still not using > them." I use exactly the settings Peter gave me in my last question. What is > in this settings wrong and where could I find the right settings? > I posted this link before: http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html The link that Peter posted has proper vdwtype and rvdw_switch settings (which say the same as the above link): http://cmb.ornl.gov/members/z8g/cheat-sheet-for-gromacs -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