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On 22/10/2010 8:21 AM, jagannath mondal wrote:
<blockquote cite="mid:89760.81912.qm@web137402.mail.in.yahoo.com"
type="cite">
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<td style="font: inherit;" valign="top">Hi,
<div> I have used gromacs 4.0.7 to do MD simulation of
two solutes A & B in water ( solvent) . </div>
<div>Initially, I had set "energy groups = system " and
used mdrun to do the simulation.</div>
<div><br>
</div>
<div>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.</div>
<div>For that I followed some discussions in mailing list
regarding using mdrun -rerun option:</div>
<div>This is what I did:</div>
<div>I used make_ndx and created 3 groups: A, B and
solvent. </div>
<div>Now, I modified the grompp.mdp file so that I have
now </div>
<div> energy groups = A B solvent </div>
<div><br>
</div>
<div>Then I used grompp -c conf -f grompp -n index -o
topol</div>
<div><br>
</div>
<div>Then I used mdrun -s -rerun traj_old.xtc </div>
<div><br>
</div>
<div>( here traj_old.xtc is the old xtc file I obtained
during the original mdrun)</div>
<div><br>
</div>
<div>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</div>
<div>I get following output </div>
<div><br>
</div>
<div><br>
</div>
<div>Here is the output from g_energy -f ener.edr :</div>
<div><br>
</div>
<div>
<div>Select the terms you want from the following list
by</div>
<div>selecting either (part of) the name or the number
or a combination.</div>
<div>End your selection with an empty line or a zero.</div>
<div>-------------------------------------------------------------------</div>
<div> 1 Bond 2 Angle 3 U-B
4 Ryckaert-Bell.</div>
<div> 5 Improper-Dih. 6 LJ-14 7
Coulomb-14 8 LJ-(SR) </div>
<div> 9 Coulomb-(SR) 10 Coul.-recip. 11
Potential 12 Kinetic-En. </div>
<div> 13 Total-Energy 14 Conserved-En. 15
Temperature 16 Pressure-(bar)</div>
<div> 17 Cons.-rmsd-() 18 Vir-XX 19 Vir-XY
20 Vir-XZ </div>
<div> 21 Vir-YX 22 Vir-YY 23 Vir-YZ
24 Vir-ZX </div>
<div> 25 Vir-ZY 26 Vir-ZZ 27
Pres-XX-(bar) 28 Pres-XY-(bar) </div>
<div> 29 Pres-XZ-(bar) 30 Pres-YX-(bar) 31
Pres-YY-(bar) 32 Pres-YZ-(bar) </div>
<div> 33 Pres-ZX-(bar) 34 Pres-ZY-(bar) 35
Pres-ZZ-(bar) 36 #Surf*SurfTen </div>
<div> 37 Mu-X 38 Mu-Y 39 Mu-Z
40 Coul-SR:A-A </div>
<div> 41 LJ-SR:A-A 42 Coul-14:A-A 43
LJ-14:A-A 44 Coul-SR:A-B </div>
<div> 45 LJ-SR:A-B 46
Coul-14:A-B </div>
<div> 47 LJ-14:A-B 48
Coul-SR:A-Solvent </div>
<div> 49 LJ-SR:A-Solvent 50
Coul-14:A-Solvent </div>
<div> 51 LJ-14:A-Solvent 52
Coul-SR:B-B </div>
<div> 53 LJ-SR:B-B 54
Coul-14:B-B </div>
<div> 55 LJ-14:B-B 56
Coul-SR:B-Solvent </div>
<div> 57 LJ-SR:B-Solvent 58
Coul-14:B-Solvent </div>
<div> 59 LJ-14:B-Solvent 60
Coul-SR:Solvent-Solvent </div>
<div> 61 LJ-SR:Solvent-Solvent 62
Coul-14:Solvent-Solvent </div>
<div> 63 LJ-14:Solvent-Solvent 64
T-System </div>
<div> 65 Xi-System</div>
</div>
<div><br>
</div>
<div>
<div>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) !! </div>
<div>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 ?</div>
</div>
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</blockquote>
<br>
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.<br>
<br>
Mark<br>
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