On 22/10/2010 8:21 AM, jagannath mondal wrote:
Hi,
I have used gromacs 4.0.7 to do MD simulation of two solutes A & B
in water ( solvent) .
Initially, I had set "energy groups = system " and used mdrun to do
the simulation.
Now,I wanted to get the potential energy contribution from due to
interaction of A-A, B-B,A-B A-solvent, B-solvent, solvent-solvent.
For that I followed some discussions in mailing list regarding using
mdrun -rerun option:
This is what I did:
I used make_ndx and created 3 groups: A, B and solvent.
Now, I modified the grompp.mdp file so that I have now
energy groups = A B solvent
Then I used grompp -c conf -f grompp -n index -o topol
Then I used mdrun -s -rerun traj_old.xtc
( here traj_old.xtc is the old xtc file I obtained during the original
mdrun)
But, now, after using this -rerun option , if I try to use the
g_energy on the resulting ener.edr file to obtain the individual
potential energy of interaction for A-A, B-B , A-B, A-solvent
I get following output
Here is the output from g_energy -f ener.edr :
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 Angle 3 U-B 4
Ryckaert-Bell.
5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR)
9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12
Kinetic-En.
13 Total-Energy 14 Conserved-En. 15 Temperature 16
Pressure-(bar)
17 Cons.-rmsd-() 18 Vir-XX 19 Vir-XY 20 Vir-XZ
21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
25 Vir-ZY 26 Vir-ZZ 27 Pres-XX-(bar) 28
Pres-XY-(bar)
29 Pres-XZ-(bar) 30 Pres-YX-(bar) 31 Pres-YY-(bar) 32
Pres-YZ-(bar)
33 Pres-ZX-(bar) 34 Pres-ZY-(bar) 35 Pres-ZZ-(bar) 36
#Surf*SurfTen
37 Mu-X 38 Mu-Y 39 Mu-Z 40
Coul-SR:A-A
41 LJ-SR:A-A 42 Coul-14:A-A 43 LJ-14:A-A 44
Coul-SR:A-B
45 LJ-SR:A-B 46 Coul-14:A-B
47 LJ-14:A-B 48 Coul-SR:A-Solvent
49 LJ-SR:A-Solvent 50 Coul-14:A-Solvent
51 LJ-14:A-Solvent 52 Coul-SR:B-B
53 LJ-SR:B-B 54 Coul-14:B-B
55 LJ-14:B-B 56 Coul-SR:B-Solvent
57 LJ-SR:B-Solvent 58 Coul-14:B-Solvent
59 LJ-14:B-Solvent 60 Coul-SR:Solvent-Solvent
61 LJ-SR:Solvent-Solvent 62 Coul-14:Solvent-Solvent
63 LJ-14:Solvent-Solvent 64 T-System
65 Xi-System
It provides me contribution from each of the energy groups on
nonbonding terms: LJ(SR),Coulomb(SR),Coulomb(14),LJ(14) . But, it
does NOT provide me their contribution to Bonding term( i.e
bond,angle, U-B,RB,improper-Dih) !!
As a result, I am a not sure how to get the net potential energy from
each of the 3 energy groups. Am I doing something wrong ? Do I need to
use any other utilities ?
Decomposing the bonded potential requires you to hack about in your .top
for some more mdrun -rerun runs. For speed, in your .mdp file set
rlist/rvdw/rcoulomb to some tiny value - this only affects non-bonded
potential, which you don't care about this time. Then remove the bonded
interactions from the .top for 2 of your groups, and a rerun will
compute the bonded interactions of the third. Rinse, repeat.
Mark
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