[gmx-users] Interaction energy..

[rama david]

Hi justin,
Ok now I get
I have to modify mdp parameter ..

Thank you,
With best wishes and regards,
Rama david

On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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