[gmx-users] Interaction energy..

[rama david]

Thank you for your Help.

I did the following tc-groups

tcoupl        = V-rescale    ; modified Berendsen thermostat
tc-grps        =  extra34 Non-Protein energy    ; two coupling groups -
more accurate
tau_t        = 0.1    0.1 0.1        ; time constant, in ps
ref_t        =  310    310 310     ; reference temperature, one for each
group, in K
;

Energy contain the residues that i needed
extra34 contain all the remaining ligand and receptor atom
non-protein contain sol and ion.

I got the energy file after mdrun -rerun

I used the g_energy term

It give me the following output
End your selection with an empty line or a zero.
-------------------------------------------------------------------
  1  G96Angle         2  Proper-Dih.      3  Improper-Dih.    4
LJ-14
  5  Coulomb-14       6  LJ-(SR)          7  LJ-(LR)          8
Disper.-corr.
  9  Coulomb-(SR)    10  Coul.-recip.    11  Potential       12
Kinetic-En.
 13  Total-Energy    14  Temperature     15  Pres.-DC        16
Pressure
 17  Constr.-rmsd    18  Box-X           19  Box-Y           20
Box-Z
 21  Volume          22  Density         23  pV              24
Enthalpy
 25  Vir-XX          26  Vir-XY          27  Vir-XZ          28
Vir-YX
 29  Vir-YY          30  Vir-YZ          31  Vir-ZX          32
Vir-ZY
 33  Vir-ZZ          34  Pres-XX         35  Pres-XY         36
Pres-XZ
 37  Pres-YX         38  Pres-YY         39  Pres-YZ         40
Pres-ZX
 41  Pres-ZY         42  Pres-ZZ         43  #Surf*SurfTen   44
Box-Vel-XX
 45  Box-Vel-YY      46  Box-Vel-ZZ      47  Mu-X            48
Mu-Y
 49  Mu-Z            50  T-extra34       51  T-non-Protein   52
T-energy
 53  Lamb-extra34                        54
Lamb-non-Protein
 55  Lamb-energy


So I confused. though it shows the energy group, which option should i have
to choose ??

What is Lamb-energy???

Is I did any mistake??? or I have to use any else command ??

Thank you in advance

With best wishes and regards.
Rama david.






On Fri, Oct 5, 2012 at 7:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/5/12 10:16 AM, rama david wrote:
>
>> Hi gromacs friends,
>>
>> I completed the simulation of receptor and ligand,
>> I visualized the trajectory in the vmd I found  most of the time C
>> terminal
>> (ARG) interact with receptor ( 320 ASP) .
>> I want to find out these interaction energy between these two residues in
>> the simulation.
>>
>>
>>
>> How to find  these interaction energy????
>>
>> ( include the LJ and electrostatic interaction)..
>>
>>
> I explained how to do this already.  You need properly set energygrps in
> the .mdp file and an index file that specifies those groups.  The
> quantities you want will then be in the .edr file like all other energy
> terms.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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