[gmx-users] Regarding g_enemat

[Justin A. Lemkul]

bipin singh wrote:
> 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.
> 

Please read the g_enemat help description again and refer to the example 
groups.dat file it provides.  You haven't set any energrygrps (in the .mdp file, 
for which certain terms are decomposed and stored in the .edr file) that 
g_enemat can act upon.  Every term listed here is simply for the entire system.

-Justin

> 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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> 
> 
> 

-- 
========================================

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

========================================