Hi, Did you see my reply last week?
Mark On Tue, Jul 31, 2018, 10:19 Vito GENNA <[email protected]> wrote: > Dear all, > > I have followed the procedure you have suggested (vide infra). > Now I have a trajectory only containing my selected atoms and its related > .tpr file. > However, after running g_energy and selecting "total energy" I get an > energy value which is too high in my opinion (i.e. 3.98246e+06 kj/mol). > I feel something is going wrong. Have you got any idea? > > Furthermore, if I would decompose this total energy in bond term, stretch > term, angle term etc etc, which would be the best way to do it? > > Thanks in advance for your contributions. > > V > > On Wed, Jul 25, 2018 at 1:32 PM, Vito GENNA <[email protected]> > wrote: > > > Dear all, > > > > I have followed the procedure you have suggested. > > Now I have a trajectory only containing my selected atoms and its related > > .tpr file. > > However, after running g_energy and selecting "total energy" I get an > > energy value which is too high in my opinion (i.e. 3.98246e+06 kj/mol). > > I feel something is going wrong. Have you got any idea? > > > > Furthermore, if I would decompose this total energy in bond term, stretch > > term, angle term etc etc, which would be the best way to do it? > > > > Thanks in advance for your contribute. > > > > V > > > > On Sun, Jul 8, 2018 at 8:06 PM, Vito GENNA <[email protected]> > > wrote: > > > >> Dear GMXusers, > >> > >> I am writing you in the hope to find a solution to my problem. > >> > >> I'd love (and truly love) calculate the intramolecular energy (both > >> bonded and non-bonded terms) of a DNA backbone for which I have a .xtc > >> trajectory (and of course coords). > >> > >> What I did: > >> > >> 1) defined the index.ndx for each DNA strand and generated a ndx.file > >> cotaining [strand-1] and [System - (strand-1)] (works fine) > >> > >> 2) Changed the energygrps in the mdp file to: [strand-1] [System - > >> (strand-1)] (works fine) > >> > >> 3) Generated a .tpr file selecting (from point 1) the .ndx of my > interest > >> > >> 4) with mdrun with -rerun option (by using the .tpr of my interest > >> generated at the previous stage) I get the .edr file [strand-1] > >> > >> 5) by using g_energy I only get Lennard-Jones and Coulomb terms (both > >> short and long for [strand-1]:[strand-1]) while I would also include the > >> bonded-terms. > >> > >> 6) The option ETOT, provided by g_energy, I guess does not return the E > >> of the strand, rather of the overall system. Isn't it? > >> > >> Since I am comparing the same system in different conditions (then in > >> different MD) I am looking for a strategy which would allow me to > >> extrapolate all the energy terms for the backbone in a consistent > fashion. > >> > >> Did you ever calculated something similar? > >> If so, how? > >> If not, any suggestion? > >> > >> Thanks in advance for all your comments. > >> > >> All the Best > >> > >> VG > >> > >> PS: Gromacs version: 5.0.4 > >> > >> -- > >> > >> *********************************************************************** > >> *Vito Genna, Ph.D* > >> > >> *Postoctoral Researcher* > >> > >> *Molecular Modeling and Bioinformatics* > >> *Orozco Lab* > >> > >> *Institute for Research in Biomedicine (IRB Barcelona)* > >> > >> *Parc Centific de Barcelona* > >> > >> *C/ Baldiri Reixac 10-12* > >> *08028 Barcelona* > >> > >> *********************************************************************** > >> > > > > > > > > -- > > > > *********************************************************************** > > *Vito Genna, Ph.D* > > > > *Postoctoral Researcher* > > > > *Molecular Modeling > <https://maps.google.com/?q=*Molecular+Modeling&entry=gmail&source=g> and > Bioinformatics* > > *Orozco Lab* > > > > *Institute for Research in Biomedicine (IRB Barcelona)* > > > > *Parc Centific de Barcelona* > > > > *C/ Baldiri Reixac 10-12* > > *08028 Barcelona* > > > > *********************************************************************** > > > > > > -- > > *********************************************************************** > *Vito Genna, Ph.D* > > *Postoctoral Researcher* > > *Molecular Modeling and Bioinformatics* > *Orozco Lab* > > *Institute for Research in Biomedicine (IRB Barcelona)* > > *Parc Centific de Barcelona* > > *C/ Baldiri Reixac 10-12* > *08028 Barcelona* > > *********************************************************************** > -- > 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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