# [gmx-users] Problem during calculating the PME contribution to linear interaction energy

Minghu Song songm at rpi.edu
Sun Feb 8 18:35:02 CET 2004

Hello, Dear gmx user,

calculating the PME constribution for llinear interaction energy.

The  average Coulomb(Long Range) for the bound ligand system form
previous MD simulation is :  -1.91894e+05.

Energies (kJ/mol)
Bond          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
1.85992e+04    1.78082e+04    5.89250e+03    5.97638e+03    2.56810e+03
LJ-14     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)
7.47750e+03    4.25080e+04    3.99207e+03   -2.02184e+03   -3.05641e+05
Coulomb (LR)      Potential    Kinetic En.   Total Energy    Temperature
-1.91894e+05   -3.94735e+05    8.19036e+04   -3.12832e+05    3.09896e+02
Pressure (bar)
6.38927e-01

In order to calculate the PME contribution, I followed the recipe
disscussed previously in the list:

Coulomb (LR, Previous)  -  [Coulomb (LR, lig_zeroq)  + Coulomb (LR,
surrounding_zeroq)], here surround is define for the all other groups
except the ligand

These are the precedure I did:
1.  Modify the original mdp file and set the constrints  = none and
nstlist =1;
2. generate a new tpr file and a new index file containing the ligand
group only -- lig.ndx by "make_ndx -f previous.pdb -o lig.ndx";
3. tpbconv -s previous.tpr -f previous.trr -n lig.ndx -o new.tpr -zeroq
4.  mdrun -s new.tpr  -rerun mprevious.trr -o new.trr -e new.edr -g new
-c new
5  g_erergy -f  new.edr -o new (then pick the Coulomb (LR) average)

So after I turned off the charge of Ligand, the new simulation results
show that now Coulomb (LR, lig_zeroq) = -384.045.
In addition,  I obtained the same results 384.045  for  the  Coulomb
(LR, surrounding_zeroq) follwing the same procedure.

Anything wrong?  Thanks for the help in advance!

jerry song
Department of Chemistry
Rensselaer Polytechnic Institute