[gmx-users] Problem in g_enemat in Gromacs 4.5.5

[rama david]

Hi Friends,
 I am working on peptide self assembly.
 I simulated two peptide which are random coil and apart from each other.
As the time process they start to interact and form antiparallel beta sheet
structure.
       My plan is to find the energy difference in random coil to beta
shhet structure.
 I added protein1 protein2 group in mdp file I run g_energy coomand


 Output:

Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
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
Coul-SR:protein1-protein1
 51  LJ-SR:protein1-protein1             52
LJ-LR:protein1-protein1
 53  Coul-14:protein1-protein1           54
LJ-14:protein1-protein1
 55  Coul-SR:protein1-protein2           56
LJ-SR:protein1-protein2
 57  LJ-LR:protein1-protein2             58
Coul-14:protein1-protein2
 59  LJ-14:protein1-protein2             60
Coul-SR:protein1-rest
 61  LJ-SR:protein1-rest                 62
LJ-LR:protein1-rest
 63  Coul-14:protein1-rest               64
LJ-14:protein1-rest
 65  Coul-SR:protein2-protein2           66
LJ-SR:protein2-protein2
 67  LJ-LR:protein2-protein2             68
Coul-14:protein2-protein2
 69  LJ-14:protein2-protein2             70
Coul-SR:protein2-rest
 71  LJ-SR:protein2-rest                 72
LJ-LR:protein2-rest
 73  Coul-14:protein2-rest               74
LJ-14:protein2-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


.But when I gave the command :


g_enemat_mpi -f ../energy.edr -groups groups.dat   -etot ener.xvg

                       I ended with following Missery :


Opened ../energy.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):protein1-protein1 (0,0)in
energy file
WARNING! could not find group (null):protein1-protein2 (0,1)in energy file
group 1WARNING! could not find group (null):protein2-protein2 (1,1)in
energy file

Will select half-matrix of energies with 6 elements
Last energy frame read 200000 time 200000.000
Will build energy half-matrix of 2 groups, 6 elements, over 200001 frames
Segmentation fault (core dumped)




I will be thankful for any suggestion.

Thank you in Advance.
With best Wishes.