[gmx-users] calculate interaction energy between two proteins

[SHAHEE ISLAM]

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
>