[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?

[Sun Yeping]

Hello Justin,

Thank you for your answer. I agree that the physical meaning of interaction
energy is questionable. Actually, the structure with the lowest interaction
energy between two groups in the trajectory is very different from what I
expect.

 Then, how should I find a structure from a MD trajectory which is most
possibly close to the real structure?  I think maybe I can select a real
crystal structure related to the structure upon which the MD simulation was
done, and use it as the reference structure, and calculate rmsd of each
frame in the trajectory against the reference structure, and find the one
with the smallest rmsd. But how to calculate the rmsd? The simulated
structure has different atom number with the reference structure, so gmx
rmsd wouldn't work. Do you know which method can work in this case?

Best wishes.

Yeping Sun

On Mon, Aug 19, 2019 at 6:59 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/18/19 11:28 PM, sunyeping wrote:
> > Hello Bratin Kumar Das，
> >
> > Your answer is correst but irrelevent to my question. By adding
> energygrps option in the mdp and rerun the trajectory and generate the edr
> file containing the interation energy information which can be extracted by
> enemat. However enemat only gives the range of the interaction energy. My
> question is how to  calculate interaction energy between two groups for
> every frame in the trajectory.
>
> That is precisely what Bratin is telling you to do, and his answer is
> exactly correct.
>
> You need to use gmx energy, not gmx enemat, to get the interaction
> energy values in every frame. Then find the lowest and extract the
> corresponding frame with trjconv. Whether or not this quantity has any
> physical meaning is, however, questionable for most force fields.
>
> -Justin
>
> > ------------------------------------------------------------------
> > From:Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> > Sent At:2019 Aug. 19 (Mon.) 11:11
> > To:gromacs <gmx-users at gromacs.org>; 孙业平 <sunyeping at aliyun.com>
> > Subject:Re: [gmx-users] How to calculate interaction energy between two
> groups for every frame in a trajectory?
> >
> > You need to prepare one .mdp file where the energygrps = DNA Protein (
> as example). Generate the .tpr file and rerun using mdrun module.
> > gmx mdrun -v -s new-tpr file -deffnm new -rerun me.xtc
> > On Mon 19 Aug, 2019, 8:09 AM sunyeping, <sunyeping at aliyun.com> wrote:
> > Dear all,
> >
> >   I am doing protein-DNA complex simulations with gromacs and I have
> gotten a trajectory. Now I want to calculate interaction energy between the
> protein and the DNA in every frame of the trajectory so that I can pick out
> a frame in which the  interaction energy between them is the largest, but I
> don't know how. I have used "enemat" , but it only gives a range of the
> energy, not every frame. The output read:
> >
> >   Last energy frame read 5000 time 500000.000
> >   Will build energy half-matrix of 2 groups, 6 elements, over 5001 frames
> >   Matrix of Coul-SR energy ranges from -18999.681641 to -1608.268188
> >   Matrix of LJ-SR energy ranges from -2540.941650 to -675.151306
> >   Matrix of total energy ranges from -21540.623047 to -2283.419434
> >
> >   So could you tell me how to calculate interaction energy between two
> groups for every frame in a trajectory?
> >
> >   Best regards.
> >   --
> >   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-request at gromacs.org.
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (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 gmx-users-request at gromacs.org.