[gmx-users] Interaction energy..
rama david
ramadavidgroup at gmail.com
Sat Oct 6 12:26:14 CEST 2012
Hi justin,
I tried as per your suggestion.
command line
g_enemat -f ener.edr -groups groups.dat -temp 310 -nolj -free
the out put is like ,
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 3 elements
Last energy frame read 50000 time 10000.000
Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
Segmentation fault (core dumped)
why program not work ?? Is it bug??? or Am I doing any stupid mistake???
Thank you in advance ..
With best wishes and regards,
Rama david
On Sat, Oct 6, 2012 at 3:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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