[gmx-users] how to include multiple energy groups for interaction energy calculation?

[Александр Лашков]

This ok. This term show non-bonded interaction for atoms
located through two valence bonds.
Alex

вт, 21 янв. 2020 г. в 10:06, sunyeping <sunyeping at aliyun.com>:

> Hi Justin,
>
> Thank you for reply. "energygrps = Protein LIG1 LIG2 LIG3 LIG4" can do the
> work. I still have a couple of questions:
>
> (1) When using the "gmx energy -f ie.edr -o ie.xvg" to extract the
> interaction energy, the interested energy terms should be input. Because
> there are four ligands in my structure, there are accordingly 16 terms, for
> example, 22 Coul-SR:Protein-LIG1, 23 LJ-SR:Protein-LIG1, 24
> Coul-14:Protein-LIG1 and 25 LJ-14-LIG1 etc.. I can input the no. of these
> 16 terms one by one as "22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37",
> but is there a simple syntax for this selection? I tried "22 to 37" and
> "22-37", but they doesn't work.
>
> (2) I find that the values of  all  Coul-14 and LJ-14 terms are zero. Does
> this make any sense?
>
> Best,
>
> Yeping Sun
> ------------------------------------------------------------------
> From:Justin Lemkul <jalemkul at vt.edu>
> Sent At:2020 Jan. 20 (Mon.) 22:17
> To:gromacs <gmx-users at gromacs.org>; 孙业平 <sunyeping at aliyun.com>
> Subject:Re: [gmx-users] how to include multiple energy groups for
> interaction energy calculation?
>
>
>
> On 1/20/20 7:58 AM, sunyeping wrote:
> > Dear all,
> >
> > I am doing MD simulations on a protein-ligand complex. This complex has
> 4  protein subunits, with each subunits binding one ligand, so there are 4
> ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have
> finished the production run and get a trajectory, and now I want to
> calculate the interaction energy between each ligand and their binding
> protein subunit, respectively. I include the  "energygrps" parameter in the
> mdp file for generating a tpr file for rerun the trajectory as following:
> >      energygrps      =  Protein LIG1
> >
> > This seems to work fine. However, could it be possible to include all
> four ligands in the "energygrps" parameter and rerun the trajectory once to
> get the interaction energy between all the four ligands and their
> respective binding protein subunit? I tried to write the "energygrps"
> parameter as following:
> >    energygrps      =  Protein LIG1, Protein LIG2, Protein LIG3, Protein
> LIG4
> > and run the "grompp" command:
> >       gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n
> index.ndx -o ie.tpr
> > I received the following error:
> >      Fatal error:
> > Group LIG1, referenced in the .mdp file was not found in the index file.
> > Group names must match either [moleculetype] names or custom index group
> > names, in which case you must supply an index file to the '-n' option
> > of grompp.
> >
> > I am sure that LIG1 is included in the index file. This error is most
> probably caused by the incorrect input of the "energygrps" parameter in the
> mdp file.
> >
> > So I wonder whether it is possible to include multiple energy groups in
> the mdp file or I have to rerun the trajectory four times to get the
> interaction energy for the four ligands?
>
> The list of energygrps should not be comma-delimited. You should specify:
>
> energygrps = Protein LIG1 LIG2 LIG3 LIG4
>
> and this will generate a full matrix of interactions among all four
> species. The LIG1-LIG2, LIG1-LIG3, etc. may not be interesting to you
> but this is how you get all of the interaction energies with the protein
> in one shot.
>
> -Justin
>
> --
> ==================================================
>
> 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.