[gmx-users] Problem in g_enemat in Gromacs 4.5.5

[Justin Lemkul]

On 7/6/13 8:21 AM, rama david wrote:
> 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)
>
>

This problem has been posted several times before and looks buggy to me.  Please 
open a redmine issue and provide a sample input file that reproduces the problem.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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