[gmx-users] Interaction energy..

[rama david]

Hi justin,

the out put of g_energy are like

-----------------------------------------------------------------
  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
Coul-SR:energy-energy
 51  LJ-SR:energy-energy                 52
LJ-LR:energy-energy
 53  Coul-14:energy-energy               54
LJ-14:energy-energy
 55  Coul-SR:energy-extra34              56
LJ-SR:energy-extra34
 57  LJ-LR:energy-extra34                58
Coul-14:energy-extra34
 59  LJ-14:energy-extra34                60
Coul-SR:energy-rest
 61  LJ-SR:energy-rest                   62
LJ-LR:energy-rest
 63  Coul-14:energy-rest                 64
LJ-14:energy-rest
 65  Coul-SR:extra34-extra34             66
LJ-SR:extra34-extra34
 67  LJ-LR:extra34-extra34               68
Coul-14:extra34-extra34
 69  LJ-14:extra34-extra34               70
Coul-SR:extra34-rest
 71  LJ-SR:extra34-rest                  72
LJ-LR:extra34-rest
 73  Coul-14:extra34-rest                74
LJ-14:extra34-rest
 75  Coul-SR:rest-rest                   76
LJ-SR:rest-rest
 77  LJ-LR:rest-rest                     78
Coul-14:rest-rest
 79  LJ-14:rest-rest                     80
T-Protein
 81  T-non-Protein                       82
Lamb-Protein
 83  Lamb-non-Protein




When I used g_enemat with the groups.dat file like these

2
extra34
energy

I got the output


roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
file
WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file
WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file
WARNING! could not find group (null):extra34-energy (0,1)in energy file
group 1WARNING! could not find group (null):energy-energy (1,1)in energy
file

Will select half-matrix of energies with 4 elements
Last energy frame read 50000 time 10000.000
Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames
Segmentation fault (core dumped)


Now When I changed the groups.dat like

2
energy
extra34

( change in the order of the index groups )

I got the following output,

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 6 elements
Last energy frame read 50000 time 10000.000
Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames
Segmentation fault (core dumped)




So What is wrong ??
Is I am doing any wrong ??



 2. I am using the temp 310 so the reference temp by default is 300 Should
I have to change it to 310

(-temp        real   300     reference temperature for free energy
calculation )

Any suggestion on these topic, is helpful to me.


Thank you in advance,



With best wishes and regards,
Rama david.