Non-visibility of energy related to CustomNonbondedForce

Automatic force field optimization. Given a force field and a set of reference data (e.g. energies and forces from QM calculations, experimental measurements), we tune the force field parameters such that it accurately reproduces the reference data.
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Robin Singh
Posts: 11
Joined: Mon Jun 19, 2023 12:25 am

Non-visibility of energy related to CustomNonbondedForce

Post by Robin Singh » Wed Sep 20, 2023 5:03 am

Dear Forcebalance developers,

I want to parameterize some LJ parameters of my system using a CustomNonbondedForce in OpenMM. I am running the calculation ad getting the below mentioned result.

Code: Select all

                             Liquid phase MD simulation #=======================================================================#
#| [92m Energy Component Analysis, Mean +- Stderr [Per Molecule] (kJ/mol) [0m |#
#=======================================================================#
HarmonicBondForce            2715.0289 +-     7.1220 [    3.6346 +-  0.0095 ] 
NonbondedForce             -66580.8270 +-    27.9331 [  -89.1310 +-  0.0374 ] 
CMMotionRemoverForce    1215.1523 +-     7.8391 [    1.6267 +-  0.0105 ] 
Potential Energy               -62650.6455 +-    25.7679 [  -83.8697 +-  0.0345 ] 
Kinetic Energy                   7523.3888 +-    17.6821 [   10.0715 +-  0.0237 ] 
Temperature                       298.6322 +-     0.7019 [    0.3998 +-  0.0009 ] 
Total Energy                     -55127.2567 +-    38.9880 [  -73.7982 +-  0.0522 ] 
-------------------------------------------------------------------------

#========================================================#
#| [1;94m            Gas phase molecular dynamics            [0m |#
#========================================================#

#=======================================================================#
#| [92m Energy Component Analysis, Mean +- Stderr [Per Molecule] (kJ/mol) [0m |#
#=======================================================================#
HarmonicBondForce               2.9327 +-     0.1718 [    2.9327 +-  0.1718 ] 
NonbondedForce               -446.2982 +-     0.1887 [ -446.2982 +-  0.1887 ] 
CustomNonbondedForce       1.2796 +-     0.1838 [    1.2796 +-  0.1838 ] 
Potential Energy                -442.0859 +-     0.3180 [ -442.0859 +-  0.3180 ] 
Kinetic Energy                      17.5865 +-     0.5531 [   17.5865 +-  0.5531 ] 
Temperature                       282.0227 +-     8.8704 [  282.0227 +-  8.8704 ] 
Total Energy                      -424.4994 +-     0.7841 [ -424.4994 +-  0.7841 ] 
-------------------------------------------------------------------------
The energy related to CustomNonbondedForce is not visible in the liquid phase simulation but it is coming only in the gas phase simulation. Why is it so?
Is the CustomNonbondedForce being processed or not?

I shall be waiting for your reply.

Regards,
Robin Singh
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User avatar
Lee-Ping Wang
Posts: 102
Joined: Sun Jun 19, 2011 5:14 pm

Re: Non-visibility of energy related to CustomNonbondedForce

Post by Lee-Ping Wang » Thu Nov 09, 2023 10:37 pm

Hello Robin,

I'm sorry for the late reply to your question. I have not attempted to optimize parameters in a CustomNonbondedForce before. I believe it is possible, but I would need a minimal test case to verify. If you are still interested in the problem, would you be willing to send me an example calculation for me to test?

Thanks,

- Lee-Ping
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