Hi All,
I'm trying to run free energy simulations for a linkage change in an
oligosaccharide when bound to its protein.
The linkage changes from beta 1-4 to beta 1-3. I followed the tutorial by
Prof Mobley.
For the lambda values I took 0 to 1 at intervals of 0.05. The values of
dVpot/dlambda from 0.00 to 0.95 seem to be in the range of E3-4. But when I
check the values of dVpot/dlambda for lambda = 1, it goes from E2 to E24 at
the end. This is only for the LBFGS minimization.
Does any one suspect a mistake in my topology or my approach?
Thanks for your time.
Sample .log file of lambda = 1 is pasted below.
Step Time Lambda
100 100.00000 1.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
1.06593e+04 8.20816e+03 2.93142e+02 4.26304e+03 8.30759e+03
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
4.13439e+04 1.92653e+05 -1.08257e+04 -1.46637e+06 -2.72128e+05
Potential Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr.
-1.48359e+06 -4.15979e+03 -1.01327e+15 0.00000e+00 0.00000e+00
Step Time Lambda
101 101.00000 1.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
1.06477e+04 8.21153e+03 2.93330e+02 4.26328e+03 8.31182e+03
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
4.13437e+04 1.92648e+05 -1.08257e+04 -1.49776e+06 -2.72128e+05
Potential Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr.
-1.51500e+06 -4.33201e+03 -2.78144e+18 0.00000e+00 0.00000e+00
Step Time Lambda
103 103.00000 1.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
1.06776e+04 8.21126e+03 2.93576e+02 4.26328e+03 8.31168e+03
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
4.13437e+04 1.92656e+05 -1.08257e+04 -1.76397e+06 -2.72128e+05
Potential Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr.
-1.78117e+06 -5.80136e+03 -1.76071e+24 0.00000e+00 0.00000e+00
Regards
Sai
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