On 1/07/2011 4:40 PM, balaji nagarajan wrote:
Dear Users !
I have took a penta peptide and did topology generation ,
I have solvated it with water box ,
now i did a minimization with zero step , to know the energy of the
initial molecule ,
i used g_energy for the out put ,
like
$ g_energy -f em.edr
it gives as follows , i have to type number to get energy !
but it lists Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
---
1 Bond 2 Angle3 Proper-Dih. 4
Ryckaert-Bell.
5 LJ-146 Coulomb-14 7 LJ-(SR) 8 LJ-(LR)
9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Pressure
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y34 Mu-Z35 T-rest
Is there any way to get the energy of the protein and the energy of
protein and water alone
There is no way to decompose the existing contents of an .edr file. You
need to use energy groups (see manual), either in your original
simulation, or "after the fact" by using mdrun -rerun on your existing
trajectory with a different .tpr.
Mark
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