The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
-
Ali Eltareb
- Posts: 39
- Joined: Tue Jul 30, 2019 10:46 am
Post
by Ali Eltareb » Wed Jan 25, 2023 12:21 pm
Hi,
I have been doing tests between Gromacs and OpenMM. I minimized a peptide using Gromacs (charmm36 forcefield). The energies that gromacs gave at the end of the minimization is
Code: Select all
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
1.67638e+01 2.25811e+01 1.28747e+02 2.69536e+00 -8.16862e-01
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
1.12933e+02 8.92176e+02 -4.19556e+01 -1.36340e+03 2.40821e+02
Potential Pressure (bar)
1.05456e+01 0.00000e+00
Steepest Descents converged to Fmax < 1000 in 4 steps
Potential Energy = 1.0545593e+01
I took this minimized configuration and read it into OpenMM using GromacsGroFile and GromacsTopFile. I checked and OpenMM is reading the configuration correctly (its not adding or removing any bonds).
Code: Select all
Potential Energy: 10.345707164397743 kJ/mol
NonbondedForce -160.00702402028134 kJ/mol
HarmonicBondForce 17.842723235913645 kJ/mol
HarmonicAngleForce 21.15079444793464 kJ/mol
PeriodicTorsionForce 129.0225362249678 kJ/mol
CustomTorsionForce 3.157813891993246 kJ/mol
CMAPTorsionForce -0.8211366161302591 kJ/mol
The energies from OpenMM are slightly different than Gromacs (they do have the same order of magnitude). The differences are about 0.2-1 kJ/mol. I want to know why the HarmonicBondForce and HarmonicAngleForce from OpenMM doesn't add up to equal Gromacs Bond and U-B term. Is there something that I am missing? Could this be a platform issue?
Ali
-
Peter Eastman
- Posts: 2564
- Joined: Thu Aug 09, 2007 1:25 pm
Post
by Peter Eastman » Wed Jan 25, 2023 3:50 pm
I suspect you're evaluating them for a slightly different conformation. Here are some things to check.
- What precision are the coordinates specified to? If it's low precision, that could lead to slight differences in the energy.
- Do you change the coordinates in any way after you set them? For example, minimizing the energy again or enforcing constraints.
- Are the periodic box dimensions set correctly?
-
Ali Eltareb
- Posts: 39
- Joined: Tue Jul 30, 2019 10:46 am
Post
by Ali Eltareb » Thu Jan 26, 2023 9:51 am
You were right, the precision of the coordinates was too low (only 3 decimal places). I used a configuration from Gromacs with more precision and the energies are in great agreement. Thanks for the help.