[gmx-users] Interaction energy..

[Justin Lemkul]

On 10/5/12 11:46 AM, rama david wrote:
> 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???
>

It is related to temperature coupling.

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

I have told you to use "energygrps" (which is described in the manual) and 
you're specifying "tc-grps."  Temperature coupling and energy calculation groups 
are very different concepts.

-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

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