On 10/5/12 11:46 AM, rama david wrote:
Thank you for your Help.
I did the following tc-groups
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = extra34 Non-Protein energy ; two coupling groups -
more accurate
tau_t = 0.1 0.1 0.1 ; time constant, in ps
ref_t = 310 310 310 ; reference temperature, one for each
group, in K
;
Energy contain the residues that i needed
extra34 contain all the remaining ligand and receptor atom
non-protein contain sol and ion.
I got the energy file after mdrun -rerun
I used the g_energy term
It give me the following output
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 T-extra34 51 T-non-Protein 52
T-energy
53 Lamb-extra34 54
Lamb-non-Protein
55 Lamb-energy
So I confused. though it shows the energy group, which option should i have
to choose ??
What is Lamb-energy???
It is related to temperature coupling.
Is I did any mistake??? or I have to use any else command ??
I have told you to use "energygrps" (which is described in the manual) and
you're specifying "tc-grps." Temperature coupling and energy calculation groups
are very different concepts.
-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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