[gmx-users] calculate interaction energy between two proteins

[Mark Abraham]

Hi,

How is the protein-protein interaction energy defined? What physical
observable is it connected to?

Mark

On Wed, Jan 9, 2019 at 9:03 AM SHAHEE ISLAM <islamshahee at gmail.com> wrote:

> can anyone please tell me, if i select 42 then wheather it will
> calculate the protein-protein interaction energy? because i did not
> define two proteins in the mdp file.i just mentioned protein.I am not
> understanding this.
> thanking you
>
> On 1/8/19, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
> > hi,
> > i want to calculate interaction energy between two protein.
> > In my system there are two proteins,waters and ions.In my .mdp file
> > the, energygrps               = PROTEIN W ION
> > i am using this command
> > gmx energy -f ../dynamic.edr -s ../eq.gro -o ener.xvg
> > then the following options are coming
> >
> > 1  Bond             2  G96Angle         3  Proper-Dih.      4
> > Improper-Dih.
> >   5  LJ-(SR)          6  Coulomb-(SR)     7  Potential        8
> > Kinetic-En.
> >   9  Total-Energy    10  Temperature     11  Pressure        12
> > Constr.-rmsd
> >  13  Box-X           14  Box-Y           15  Box-Z           16  Volume
> >  17  Density         18  pV              19  Enthalpy        20  Vir-XX
> >  21  Vir-XY          22  Vir-XZ          23  Vir-YX          24  Vir-YY
> >  25  Vir-YZ          26  Vir-ZX          27  Vir-ZY          28  Vir-ZZ
> >  29  Pres-XX         30  Pres-XY         31  Pres-XZ         32  Pres-YX
> >  33  Pres-YY         34  Pres-YZ         35  Pres-ZX         36  Pres-ZY
> >  37  Pres-ZZ         38  #Surf*SurfTen   39  Box-Vel-XX      40
> Box-Vel-YY
> >  41  Box-Vel-ZZ                          42  Coul-SR:Protein-Protein
> >  43  LJ-SR:Protein-Protein               44  Coul-SR:Protein-W
> >  45  LJ-SR:Protein-W                     46  Coul-SR:Protein-ION
> >  47  LJ-SR:Protein-ION                   48  Coul-SR:W-W
> >  49  LJ-SR:W-W                           50  Coul-SR:W-ION
> >  51  LJ-SR:W-ION                         52  Coul-SR:ION-ION
> >  53  LJ-SR:ION-ION   54  T-Protein       55  T-W             56  T-ION
> >  57  Lamb-Protein    58  Lamb-W          59  Lamb-ION
> >
> > if i select 42 and 43. will it give me the total energy value
> > considering both proteins.
> > or what should i correctly select.
> > thanking you
> > Shahee Islam
> >
> --
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