Sorry it was a typing mistake..it is actually 1] To make indexes:- gmx make_ndx -f md.gro -o Hn-OW.ndx
> del 2 Removed group 2 'SOL' > del 1 Removed group 1 'Water' > del 0 Removed group 0 'System' > a H1 H2 H3 OW Found xxx atoms with name H1 H2 H3 OW 0 H1 H2 H3 OW : xxx atoms > q 2]Then, Using the index to calculate the pair correlation function for all frames:- gmx rdf -f md.trr -s md.tpr -n Hn-OW.ndx -o rdf_Hn-OW.xvg Available static index groups: Group 0 "H1_H2_H3 OW" (xxx atoms) Specify a selection for option 'ref' (Reference selection for RDF computation): (one per line, <enter> for status/groups, 'help' for help) > 0 Selection '0' parsed >cntrl+d Last frame 1000 time 10000.000 Analyzed 1001 frames, last time 10000.000 3] View the plot: xmgrace rdf_Hn-OW.xvg and if i view the obtained graphs in xmgrace i am getting only two kinds of graphs...ie., (a) for Hn-OW,Ha-OW etc, graphs are same for OW end indexing and (b) for Hn-HW,Ha-HW etc., graphs are same for HW end indexing.. My doubts are.. 1)What is this only two kinds of graphs am i getting..?? , 2)I hope the above procedure to get RDF ie., commands 1] gmx make_ndx....., 2] gmx rdf ..... 3] xmgrace..... are correct in accordance.. 3)Or is there any mistake that i am doing..?? Can anybody rectify my mistakes if any..?? as you have told how to put Hn atoms in one group and the Ow in another...?? <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> On Tue, Mar 28, 2017 at 2:10 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/27/17 3:55 PM, Dilip H N wrote: > >> i want to calculate RDF of glycine of Hn-OW, Hn-HW, Ha-OW, Ha-HW, Ca-OW, >> etc., >> So my commands were as follows... >> >> 1] To make indexes:- >> gmx make_ndx -f md.gro -o Hn-OW.ndx >> >> del 2 >>> >> Removed group 2 'SOL' >> > del 1 >> Removed group 1 'Water' >> > del 0 >> Removed group 0 'System' >> >>> a H1 H2 H3 OW >>> >> Found xxx atoms with name H1 H2 H3 OW >> 0 HA1_HA2_OW : xxx atoms >> >>> q >>> >> >> >> 2]Then, Using the index to calculate the pair correlation function for all >> frames:- >> gmx rdf -f md.trr -s md.tpr -n Hn-OW.ndx -o rdf_Hn-OW.xvg >> >> Available static index groups: >> Group 0 "HA1_HA2_OW" (xxx atoms) >> Specify a selection for option 'ref' >> (Reference selection for RDF computation): >> (one per line, <enter> for status/groups, 'help' for help) >> >>> 0 >>> >> Selection '0' parsed >> >>> cntrl+d >>> >> Last frame 1000 time 10000.000 >> Analyzed 1001 frames, last time 10000.000 >> >> 3] View the plot: >> >> xmgrace rdf_Hn-OW.xvg >> >> and if i view the obtained graphs in xmgrace i am getting only two kinds >> of >> graphs...ie., >> (a) for Hn-OW,Ha-OW etc, graphs are same for OW end indexing and >> (b) for Hn-HW,Ha-HW etc., graphs are same for HW end indexing.. >> >> My doubts are.. >> 1)What is this only two kinds of graphs am i getting..?? , >> 2)I hope the above procedure to get RDF ie., commands 1] gmx >> make_ndx....., >> 2] gmx rdf ..... 3] xmgrace..... are correct in accordance.. >> 3)Or is there any mistake that i am doing..?? Can anybody rectify my >> mistakes if any..?? >> >> > You're probably just getting a bunch of garbage. You're apparently > merging the alpha hydrogen atoms and water oxygens into one group, which > makes no sense at all. If you want Ha-Ow RDF, then the Ha* atoms should be > in one group and the Ow in another. > > -Justin > > >> >> >> >> <https://mailtrack.io/> Sent with Mailtrack >> <https://mailtrack.io/install?source=signature&lang=en&refer >> ral=cy16f01.di...@nitk.edu.in&idSignature=22> >> >> On Mon, Mar 27, 2017 at 10:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 3/27/17 8:50 AM, Dilip H N wrote: >>> >>> Thanks Justin, >>>> >>>> But my doubts are.. >>>> 1] after energy minimization of both glycine non zwitterionic form and >>>> zwitterionic form with water, if i visualize it in vmd, the bond between >>>> some of the water molecules are broken.. why is this so..?? >>>> >>>> >>> http://www.gromacs.org/Documentation/Terminology/Periodic_ >>> Boundary_Conditions >>> >>> What you see on the VMD display is its best guess as to how things are >>> connected. That's not always right. The topology is always right. >>> That's >>> why trjconv exists. >>> >>> 2] and ran nvt,npt,md simulations respectively...and during analysis >>> part i >>> >>>> am getting only similar two types of RDF graphs...why is this >>>> happening...i >>>> have made all the indexing, etc., proper... >>>> >>>> >>>> You have provided no useful information about what these RDF plots are >>> or >>> how you acquired them, so there's no point for either of us in guessing. >>> Maybe the distribution(s) that you're looking at simply don't vary as a >>> function of protonation state. >>> >>> Is there any tutorials for these as an example..?? solving this would >>> help >>> >>>> me a lot.... >>>> >>>> >>>> It's an amino acid in water; it's as easy of a protein system as there >>> is. >>> There's nothing special about it that requires a tutorial. >>> >>> -Justin >>> >>> >>> <https://mailtrack.io/> Sent with Mailtrack >>>> <https://mailtrack.io/install?source=signature&lang=en&refer >>>> ral=cy16f01.di...@nitk.edu.in&idSignature=22> >>>> >>>> >>>> On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>> >>>> >>>>> On 3/23/17 2:05 PM, Dilip H N wrote: >>>>> >>>>> Hello, >>>>> >>>>>> >>>>>> I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and >>>>>> in >>>>>> the first step if i do the energy minimization and then visualizes the >>>>>> mixture, the glycine is no more in its pure form as before instead it >>>>>> has >>>>>> been converted to its zwitter ionic form [NH3CH2COO], and some >>>>>> Hydrogen >>>>>> bonds with water are also broken. How can i solve these both >>>>>> issues..?? >>>>>> >>>>>> >>>>>> Glycine didn't convert between forms. That's impossible; bonds can't >>>>>> >>>>> break or form in a molecular mechanical process. The termini are >>>>> exactly >>>>> what you assigned them to be. If you want them to be something else, >>>>> you >>>>> have to assign them as such with pdb2gmx. Though you should note that >>>>> NH2 >>>>> and COOH can't coincide at any real pH value. >>>>> >>>>> -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. > -- With Best Regards, DILIP.H.N Ph.D Student -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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