Hi Peter,

This is a new OpenMM magic that I was not aware of!

Thank you so much for your help and support.

Gaetano

Hi there, In my system, I’m using positional restraints by adding a Custom External Force like the following: openmm.CustomExternalForce('k_restr*( (x-x0)^2 + (y-y0)^2 + (z-z0)^2 )') where the per particle parameters x0, y0 and z0 are taken from my starting structure positions. I’m performing a NVT ...

Hi Peter,

Thanks a lot for your help...everything works now!

Gaetano

Hi there, I was trying to understand how virtual site works in OpenMM but I'm not sure if I'm doing the correct setting. I have an ethylene molecule than I would like to simulate in vacuum. The system has been created with Amber and I have attached the topology, coordinate files and the script that ...

Hi Peter,
Thanks for your reply. Yes you're right I was trying to make something wrong.
Cheers,
Gaetano

Hi Peter,

Thanks for your prompt reply. What can I do if I want to scale the 1-4 interactions and I cannot use the CustomBonded class because of the lack of PBC conditions? Is there an easy way?

Thanks a lot

Gaetano

Hi There, I would like to extend the CustomNonBonded Force class to support the createExceptionsFromBonds() method. My idea is to copy and adapt the needed code from the standard NonBonded class which presents this method. Are there technical issues that I should be aware before embarking in this ex...

Hi Peter,

Thanks a lot for your help and support. I'll try to write a plug in.

Cheers,

Gaetano

Dear Peter, Thanks for your prompt reply. I'm trying to implement the single topology method (alchemical transformations) for the calculation of free energy changes. To do so I have defined hard, to dummy and from dummy solute atoms. These groups of atoms interact differently with the solvent molecu...

Hi there, I wonder if CustomNonBonded forces still need to be applied on the same particles and on the same Exclusion/Exception list in OpenMM 5.0. If I decided to learn how to write a new plugin in OpenMM what can I gain in terms of implementation of different non bonded forces applied to different...