[gmx-users] calculate interaction energy between two proteins

[SHAHEE ISLAM]

it is connected with aggregation phenomenon.

On 1/9/19, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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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