[gmx-users] Problem during calculating the PME contribution to linear interaction energy
songm at rpi.edu
Sun Feb 8 18:35:02 CET 2004
Hello, Dear gmx user,
Thank David for answer about g_lie. I met another problem during
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.
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
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
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
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!
Department of Chemistry
Rensselaer Polytechnic Institute
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