[gmx-users] Regarding g_enemat

[bipin singh]

Thanks for your reply

The following terms are present in my energy files

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

So, please suggest why I am getting error, If the LJ-(SR) and Coulomb-(SR)
terms are already present in the energy file.

On Thu, Apr 14, 2011 at 00:36, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> bipin singh wrote:
>>
>> Hello,
>>
>> I am using g_enemat to calculate the energy matrix from the energy
>> file(edr file) and I am supplying Protein as a group in -groups
>> option.
>> The command I am supplied is as follows:
>>
>> g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot
>> energy.xvg -temp 328 -nocoul -nolj -nomean
>>
>> but I am getting the following error
>> Read 1 groups
>> group 0WARNING! could not find group (null):Protein-Protein (0,0)in energy
>> file
>>
>> As written in the manual:
>> "Energy groups with names like ’Coul-SR:Protein-SOL’ and
>> ’LJ:Protein-SOL’ are expected in the energy
>> file"
>> But I am not clear how to get these terms in energy file.....
>>
>
> Whatever name you supply has to be an actual term in the .edr file.  Run
> g_energy first to get a list of all valid energy terms if you are unfamiliar
> with the contents of the .edr file.
>
> -Justin
>
>> The energy file I am supplying is from a 100 ns md simulation.
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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-- 
-----------------------
Regards,
Bipin Singh