[gmx-users] Problem in g_enemat in Gromacs 4.5.5

[Mark Abraham]

And please replicate it with a more recent 4.5.x or 4.6.x first!

Mark

On Sun, Jul 7, 2013 at 3:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ==================================================
>
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