[gmx-users] About g_enemat problem

[rama david]

---------- Forwarded message ----------
From: rama david <ramadavidgroup at gmail.com>
Date: Wed, Dec 26, 2012 at 9:55 PM
Subject: About g_enemat problem
To: gmx-users-owner at gromacs.org


Hi Gromacs friend.

I simulated a system containing random peptide
I found that as they start to interact they change there secondary conformation.

I want to determine the interaction potential energy of two peptide only.
I make new mdp file containing  the energygrps protein1 and protein2
I rerun the mdrun
Now When I gave the command g_enemat it replied like

Opened md-rerun.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 100000 time 100000.000
Will build energy half-matrix of 2 groups, 6 elements, over 100001 frames
Segmentation fault (core dumped)


I face the same problem in another system also...




but when I wrote the command g_energy I received


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-SOL
 61  LJ-SR:protein1-SOL                  62  LJ-LR:protein1-SOL
 63  Coul-14:protein1-SOL                64  LJ-14:protein1-SOL
 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-SOL
 71  LJ-SR:protein2-SOL                  72  LJ-LR:protein2-SOL
 73  Coul-14:protein2-SOL                74  LJ-14:protein2-SOL
 75  Coul-SR:SOL-SOL                     76  LJ-SR:SOL-SOL
 77  LJ-LR:SOL-SOL                       78  Coul-14:SOL-SOL
 79  LJ-14:SOL-SOL   80  T-Protein       81  T-non-Protein   82  Lamb-Protein
 83  Lamb-non-Protein





Where am I wrong ???

Is there any other way to do these ???





I also want to check the change in entropy of sol and protein ..How to
check it ???

Please give me the suggestion.I will be a very thankfull to you.

With Best Wishes and regards,
Rama david