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Non-visibility of energy related to CustomNonbondedForce

Posted: Wed Sep 20, 2023 5:03 am
by singh
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

Re: Non-visibility of energy related to CustomNonbondedForce

Posted: Thu Nov 09, 2023 10:37 pm
by leeping
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