Hi, On Tue, Jul 24, 2018, 12:33 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? > No. What value would be appropriate, and why? 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? > You can edit the topology before you give it to grompp if the default decomposition isn't suitable for you. But I know of no use for such a decomposition, nor a force field that was parameterized with such a use case in mind. Mark Thanks in advance for your contribute. > > V > > On Sun, Jul 8, 2018 at 8:17 PM, Vito GENNA <[email protected]> > wrote: > > > Dear Justin, > > > > Thanks a lot. > > I indeed did not consider the idea to extrapolate only a part of the > whole > > trajectory. Nice shot. > > Well, regarding the forcefield, this calculation in part is aiming to a > > kind of “ff validation”. > > > > Thanks a lot for your prompt reply. > > > > V > > > > *Vito Genna, Ph.D* > > PostDoctoral Researcher > > Molecular Modelling and Bioinformatics > > Orozco Lab > > > > *Dep. of Structural and Computational Biology* > > *Institute for Research in Biomedicine (IRB Barcelona)* > > Parc Científic de > <https://maps.google.com/?q=Parc+Cient%C3%ADfic+de+&entry=gmail&source=g> > Barcelona > > C/ Baldiri Reixac 10-12 > > 08028 Barcelona > > > > P.S. This message has been written with my IPhone. Sorry for typo. > > > > Il giorno 08 lug 2018, alle ore 20:12, Justin Lemkul <[email protected]> > ha > > scritto: > > > > > > > > On 7/8/18 2:06 PM, Vito GENNA 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? > > > > > > You need to extract only the coordinates you want from the trajectory > with > > trjconv and your index group. Then, create a matching .tpr file with only > > those atoms using convert-tpr. Then use mdrun -rerun. Whether or not the > > quantity means anything depends on how your force field was parametrized, > > but that's how you calculate it. > > > > -Justin > > > > If not, any suggestion? > > > > > > Thanks in advance for all your comments. > > > > > > All the Best > > > > > > VG > > > > > > PS: Gromacs version: 5.0.4 > > > > > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Virginia Tech Department of Biochemistry > > > > 303 Engel Hall > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > [email protected] | (540) 231-3129 > > http://www.thelemkullab.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 [email protected]. > > > > > > > -- > > *********************************************************************** > *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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