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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