Why are you using PME-switch? Without explicitly choosing a switch? Mark
On Thu, Dec 12, 2013 at 6:45 PM, mcfc1301 <mcfc1...@gmail.com> wrote: > Hello Everyone, > > I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot > but > find little useful. > My Gromacs was installed in a Linux cluster. > > Follows is my steps to do normal mode analysis: > > • pdb2gmx -ignh -ff < forcefield > -f <protein.pdb> -o mut.gro -p topol.top > • editconf -f mut.gro -o box.gro -d 1.5 > • grompp -f em.mdp -c box.gro -p topol.top -o em.tpr > • mdrun -s em.tpr -deffnm em -c em.g96 -v > • grompp -f nm.mdp -c em.g96 -o nm.tpr > --------------->WARNING 1 [file nm.mdp]: > The switching range for PME-Switch should be 5% or > less, energy > conservation will be good anyhow, since ewald_rtol > = > 1e-05 > > I have taken advises from the forum that I should not genbox and should use > cg instead steep for em in order to do Normal Mode Analysis, but now I am > facing problem of PME-Switch. > > Does anyone have any experience on this? > > Thanks in advance. > > Kevin > > > ==============Attached is em.mdp and nm.mdp========================= > em.mdp > > define = -DFLEXIBLE > constraints = none > integrator = cg > dt = 0.002 ; ps ! > nsteps = 400 > nstlist = 10 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > vdwtype = cut-off > rvdw = 1.4 > optimize_fft = yes > emtol = 1000 > emstep = 0.01 > > --------------------------------------- > nm.mdp > constraints = none > integrator = nm > dt = 0.002 ; ps ! > nsteps = 400 > nstlist = 10 > ns_type = grid > rlist = 1.2 > coulombtype = PME-Switch > rcoulomb = 1.0 > vdwtype = Cut-off > rvdw = 1.4 > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Normal-Mode-Analysis-with-Gromacs-4-6-tp5013240p5013276.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.