bipin singh wrote:
Thanks for your reply
The following terms are present in my energy files
1 Angle 2 Proper-Dih. 3 Improper-Dih. 4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr. 8 Coulomb-(SR)
9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy
13 Temperature 14 Pres.-DC 15 Pressure 16 Constr.-rmsd
17 Box-X 18 Box-Y 19 Box-Z 20 Volume
21 Density 22 pV 23 Enthalpy 24
Vir-XX
25 Vir-XY 26 Vir-XZ 27 Vir-YX 28
Vir-YY
29 Vir-YZ 30 Vir-ZX 31 Vir-ZY 32
Vir-ZZ
33 Pres-XX 34 Pres-XY 35 Pres-XZ 36 Pres-YX
37 Pres-YY 38 Pres-YZ 39 Pres-ZX 40 Pres-ZY
41 Pres-ZZ 42 #Surf*SurfTen 43 Box-Vel-XX 44 Box-Vel-YY
45 Box-Vel-ZZ 46 Mu-X 47 Mu-Y 48 Mu-Z
49 T-Protein 50 T-non-Protein
51 Lamb-Protein 52 Lamb-non-Protein
So, please suggest why I am getting error, If the LJ-(SR) and Coulomb-(SR)
terms are already present in the energy file.
Please read the g_enemat help description again and refer to the example
groups.dat file it provides. You haven't set any energrygrps (in the .mdp file,
for which certain terms are decomposed and stored in the .edr file) that
g_enemat can act upon. Every term listed here is simply for the entire system.
-Justin
On Thu, Apr 14, 2011 at 00:36, Justin A. Lemkul <[email protected]> wrote:
bipin singh wrote:
Hello,
I am using g_enemat to calculate the energy matrix from the energy
file(edr file) and I am supplying Protein as a group in -groups
option.
The command I am supplied is as follows:
g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot
energy.xvg -temp 328 -nocoul -nolj -nomean
but I am getting the following error
Read 1 groups
group 0WARNING! could not find group (null):Protein-Protein (0,0)in energy
file
As written in the manual:
"Energy groups with names like ’Coul-SR:Protein-SOL’ and
’LJ:Protein-SOL’ are expected in the energy
file"
But I am not clear how to get these terms in energy file.....
Whatever name you supply has to be an actual term in the .edr file. Run
g_energy first to get a list of all valid energy terms if you are unfamiliar
with the contents of the .edr file.
-Justin
The energy file I am supplying is from a 100 ns md simulation.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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