thank you for answers after this command :grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr i receive 2 note :
NOTE 1 [file topol.top, line 927]: System has non-zero total charge: 4.000000 Total charge should normally be an integer. should i add ion ? with ion.itp that is in gromos53a6_lipid.ff ? NOTE 2 [file minim.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing .what is it's reason and what should i do ?.i used from same minim.mdp file that was for dppc( in tutorial.) should i change cut off ?on what basis? i don't find it in manual On Fri, Jul 15, 2016 at 6:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/15/16 9:55 AM, roshanak starlight wrote: > >> excuse me.i don't understand . should i update [molecule] just in >> *topol.top* ? how? >> my topol.top file in [molecule] has not any number : >> >> [ molecules ] >> ; Compound #mols >> Protein 1 >> >> > Add a line that says "DPPC 126" > > You have to manually account for changes that are being made to the > coordinate file. Please do some more basic tutorial material if the > content and organization of a topology is unfamiliar to you. > > -Justin > > > in my topol_dppc.top is this: >> >> [ molecules ] >> ; molecule name nr. >> DPPC 128 >> SOL 3655 >> >> >> >> On Fri, Jul 15, 2016 at 6:12 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 7/15/16 9:40 AM, roshanak starlight wrote: >>> >>> should i do this ? : >>>> i should change dppc from 128lipid (topol_dppc.top) to 6300atom and >>>> >>>> >>> topol_dppc.top is only ever used for making molecules whole, and never >>> again. >>> >>> system_inflated.gro from 6348 t0 6300 ? >>> >>>> >>>> >>> Do not change the .gro file at all. >>> >>> but why is number of system.gro 6538 ? (6400 + 138) >>> >>>> >>>> >>> In system.gro (and the corresponding topol.top) you have 128 lipids and >>> the peptide. Then InflateGRO removes two of those lipids, so you have to >>> account for this in topol.top, which now has the peptide and 126 lipids. >>> >>> -Justin >>> >>> >>> 50 is atom per lipid >>> >>>> >>>> >>>> On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>> >>>> >>>>> On 7/15/16 9:26 AM, roshanak starlight wrote: >>>>> >>>>> hello . when i want to do energy minimizationin step 3 , with this >>>>> >>>>>> command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o >>>>>> em.tpr >>>>>> (or confout.gro replace em.tpr) i face with this error: >>>>>> >>>>>> Fatal error: >>>>>> number of coordinates in coordinate file (system_inflated.gro, 6438) >>>>>> does not match topology (topol.top, 138) >>>>>> >>>>>> Earlier, right after this command : perl inflategro.pl system.gro 4 >>>>>> DPPC >>>>>> 14 >>>>>> system_inflated.gro 5 area.dat >>>>>> , i updated [molecules] in topol-dppc.top from 128 to 126 dppc >>>>>> (because >>>>>> of >>>>>> this sentence in terminal: >>>>>> There are 2 lipids within cut-off range... >>>>>> 1 will be removed from the upper leaflet... >>>>>> 1 will be removed from the lower leaflet...) >>>>>> >>>>>> where is the problem from ? >>>>>> >>>>>> >>>>>> Apparently you didn't actually update the topology. >>>>>> >>>>> >>>>> 126 * 50 = 6300 >>>>> 6438 - 138 = 6300 >>>>> >>>>> So your topology specifies no lipids. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul <jalem...@vt.edu> >>>>> wrote: >>>>> >>>>> >>>>>> >>>>>> >>>>>> On 7/15/16 4:56 AM, roshanak starlight wrote: >>>>>>> >>>>>>> excuse me i forgot that write subject. >>>>>>> >>>>>>> >>>>>>>> On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight < >>>>>>>> starlight....@gmail.com >>>>>>>> >>>>>>>> wrote: >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> hello >>>>>>>>> >>>>>>>> >>>>>>>> i use kalp-15 in dppc tutorial that there is in this website : >>>>>>>> >>>>>>>>> http://www.bevanlab.biochem.vt.edu >>>>>>>>> i have 2 question about step 3 : >>>>>>>>> 1.after this command : genrestr -f KALP_newbox.gro -o >>>>>>>>> strong_posre.itp >>>>>>>>> -fc 100000 100000 100000 which shoud i choose ? ( i choose >>>>>>>>> 1:protein . >>>>>>>>> is it right ?) >>>>>>>>> >>>>>>>>> >>>>>>>>> From the tutorial: >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> "The authors of the InflateGRO script recommend using a very strong >>>>>>> position-restraining force on protein heavy atoms to ensure that the >>>>>>> position of the protein does not change during EM." >>>>>>> >>>>>>> So choose the protein heavy atoms (Protein-H). >>>>>>> >>>>>>> 2.where should i add a line "define = -DSTRONG_POSRES" in minim.mdp >>>>>>> ? >>>>>>> i >>>>>>> >>>>>>> add it (define = -DSTRONG_POSRES ) to end of my file . is it true? >>>>>>> >>>>>>>> >>>>>>>> thank you >>>>>>>>> >>>>>>>>> >>>>>>>>> It doesn't matter. >>>>>>>>> >>>>>>>>> >>>>>>>> -Justin >>>>>>> >>>>>>> -- >>>>>>> ================================================== >>>>>>> >>>>>>> Justin A. Lemkul, Ph.D. >>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>>>> >>>>>>> Department of Pharmaceutical Sciences >>>>>>> School of Pharmacy >>>>>>> Health Sciences Facility II, Room 629 >>>>>>> University of Maryland, Baltimore >>>>>>> 20 Penn St. >>>>>>> Baltimore, MD 21201 >>>>>>> >>>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>>>> http://mackerell.umaryland.edu/~jalemkul >>>>>>> >>>>>>> ================================================== >>>>>>> -- >>>>>>> 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. >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>> ================================================== >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>> >>>>> Department of Pharmaceutical Sciences >>>>> School of Pharmacy >>>>> Health Sciences Facility II, Room 629 >>>>> University of Maryland, Baltimore >>>>> 20 Penn St. >>>>> Baltimore, MD 21201 >>>>> >>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>> http://mackerell.umaryland.edu/~jalemkul >>>>> >>>>> ================================================== >>>>> -- >>>>> 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. >>>>> >>>>> >>>>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> 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. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.
