[gmx-users] Interaction energy..

[Justin Lemkul]

On 10/6/12 2:28 AM, rama david wrote:
> 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)
>
>

Based on the energy names, this is the appropriate setup, but unfortunately I 
have no idea why it does not work.  I have noticed that there is a problem with 
g_enemat - the -lj flag specifies both LJ-SR and LJ-LR terms to be written - 
which may be complicating matters.  Please try your command with -nolj to test.

>
>
> 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 )
>

As stated in the description, the -temp option is for free energy calculations. 
  Are you requesting a free energy calculation?  You haven't provided your 
command line.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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