How would I know what coordinate file to use? I have been following the tutorial word for word. However, I did not get the confout.gro file that I should have gotten after the minimization (mdrun -v -deffnm em) so I have been using em.gro. Would this be a problem? ________________________________ From: Justin A. Lemkul [via GROMACS] [[email protected]] Sent: Friday, June 08, 2012 5:42 PM To: Hicks, Erica Subject: RE: Energy Minimization - not getting correct lipid area
On 6/8/12 6:33 PM, Erica Hicks wrote: > Hi, > > bash-3.2$ perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 > area.dat > Reading..... > Scaling lipids.... > There are 128 lipids... > with 50 atoms per lipid.. > > Determining upper and lower leaflet... > 64 lipids in the upper... > 64 lipids in the lower leaflet > > Centering protein.... > Checking for overlap.... > ...this might actually take a while.... > 100 % done... > There are 2 lipids within cut-off range... > 1 will be removed from the upper leaflet... > 1 will be removed from the lower leaflet... > > Writing scaled bilayer& centered protein... > > > Calculating Area per lipid... > Protein X-min/max: 26 40 > Protein Y-min/max: 25 39 > X-range: 14 A Y-range: 14 A > Building 14 X 14 2D grid on protein coordinates... > Calculating area occupied by protein.. > full TMD.. > upper TMD.... > lower TMD.... > Area per protein: 2 nm^2 > Area per lipid: 10.4716089904762 nm^2 > > Area per protein, upper half: 1.75 nm^2 > Area per lipid, upper leaflet : 10.4755772444444 nm^2 > > Area per protein, lower half: 2 nm^2 > Area per lipid, lower leaflet : 10.4716089904762 nm^2 > > Writing Area per lipid... > Done! > > bash-3.2$ mdrun -v -deffnm em > Back Off! I just backed up em.log to ./#em.log.6# > Getting Loaded... > Reading file em.tpr, VERSION 4.5.4 (single precision) > Starting 4 threads > Loaded with Money > > Making 1D domain decomposition 4 x 1 x 1 > > Back Off! I just backed up em.trr to ./#em.trr.6# > > Back Off! I just backed up em.edr to ./#em.edr.6# > > Steepest Descents: > Tolerance (Fmax) = 1.00000e+03 > Number of steps = 50000 > Step= 0, Dmax= 1.0e-02 nm, Epot= -3.06212e+05 Fmax= 5.37269e+03, atom= 3275 > Step= 1, Dmax= 1.0e-02 nm, Epot= -3.10498e+05 Fmax= 2.40668e+03, atom= 3024 > Step= 3, Dmax= 6.0e-03 nm, Epot= -3.10958e+05 Fmax= 2.89119e+03, atom= 4225 > Step= 5, Dmax= 3.6e-03 nm, Epot= -3.12589e+05 Fmax= 1.46767e+03, atom= 1365 > Step= 6, Dmax= 4.3e-03 nm, Epot= -3.13033e+05 Fmax= 3.83969e+03, atom= 1365 > Step= 7, Dmax= 5.2e-03 nm, Epot= -3.13599e+05 Fmax= 2.88720e+03, atom= 1365 > Step= 8, Dmax= 6.2e-03 nm, Epot= -3.13688e+05 Fmax= 4.93154e+03, atom= 1365 > Step= 9, Dmax= 7.5e-03 nm, Epot= -3.14101e+05 Fmax= 4.72541e+03, atom= 1365 > Step= 11, Dmax= 4.5e-03 nm, Epot= -3.14800e+05 Fmax= 9.90227e+02, atom= 1365 > > writing lowest energy coordinates. > > Back Off! I just backed up em.gro to ./#em.gro.6# > > Steepest Descents converged to Fmax< 1000 in 12 steps > Potential Energy = -3.1480012e+05 > Maximum force = 9.9022711e+02 on atom 1365 > Norm of force = 1.2180042e+02 > > > bash-3.2$ perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 > area_shrink1.dat > Reading..... > Scaling lipids.... > There are 128 lipids... Something is wrong here. You should only have 126 lipids since 2 were removed before. Did you minimize the correct coordinate file? > with 50 atoms per lipid.. > > Determining upper and lower leaflet... > 64 lipids in the upper... > 64 lipids in the lower leaflet > > No protein coordinates found... This is also strange. This, coupled with the lines above regarding the number of lipids, suggest you're using the wrong coordinate file. > Writing scaled bilayer& centered protein... > > > Calculating Area per lipid... > Protein X-min/max: 10000 -9999 > Protein Y-min/max: 10000 -9999 > X-range: -19999 A Y-range: -19999 A > Building -19999 X -19999 2D grid on protein coordinates... > Calculating area occupied by protein.. > full TMD.. > upper TMD.. > lower TMD.. The following areas are meaningless, for reasons associated with incorrect content or processing thereof. > Area per protein: 0 nm^2 > Area per lipid: 0.583197761890625 nm^2 > > Area per protein, upper half: 0 nm^2 > Area per lipid, upper leaflet : 0.583197761890625 nm^2 > > Area per protein, lower half: 0 nm^2 > Area per lipid, lower leaflet : 0.583197761890625 nm^2 > > Writing Area per lipid... > Done! > > To me, it looks like it is not looking at the 126 lipids that I updated in > the topology file. Hmmmm.... OK, I seem to remember 124 being what my system produced, but that's irrelevant. Check out the lines above. > Erica > > ________________________________ > From: Justin A. Lemkul [via GROMACS] [[hidden email]<UrlBlockedError.aspx>] > Sent: Friday, June 08, 2012 5:21 PM > To: Hicks, Erica > Subject: RE: Energy Minimization - not getting correct lipid area > > > > On 6/8/12 6:18 PM, Erica Hicks wrote: >> Hi, >> >> Everything should be updated correctly. I added in the DPPC 128 underneath >> the protein in [molecules] but I still get the same results. What do you mean >> by " Further manual modifications are necessary based on how many lipids >> InflateGRO removes"? After I generated the new position restrain file, I >> updated the minim.mdp withe the correct info. I then scaled by a factor of 4, >> updated [molecules], ran energy minimization (mdrun -v -deffnm em), and > > This is all my comment meant. If InflateGRO removes 4 lipids, then you have > 124 > left, which it sounds like you have accounted for. > >> scaled by a factor 0.95. I have no idea what could possibly going wrong. >> Maybe something with the manipulation of InflateGRO???? > > Please provide the entire screen output of the first shrinking step that > InflateGRO produces. > > -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 [hidden email]<UrlBlockedError.aspx> > 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 [hidden email]<UrlBlockedError.aspx>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ________________________________ > If you reply to this email, your message will be added to the discussion > below: > > NAML<<UrlBlockedError.aspx>http://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Energy-Minimization-not-getting-correct-lipid-area-tp4998235p4998245.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- ======================================== Justin A. 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