Search found 6 matches
- Mon Nov 28, 2016 2:15 pm
- Forum: OpenMM
- Topic: Reporting specific force groups
- Replies: 2
- Views: 149
Re: Reporting specific force groups
Peter, thanks for your quick response. A few more questions: 1. Is there a way to get the MI distance between groups? I would call state.getPeriodicBoxVectors() and use the side lengths in a custom distance function and manually calculate COMs for g1, g2 etc. also from a custom function. A periodicd...
- Mon Nov 28, 2016 2:33 am
- Forum: OpenMM
- Topic: Reporting specific force groups
- Replies: 2
- Views: 149
Reporting specific force groups
I have a system with a COM force between two groups that is in a separate force group, 1. All other forces are in group 0. To report only forces from group 0, one would call `system.getState(..., groups={0})`. My question is if this can be done using a Reporter? From the manual example, class ForceR...
- Mon Aug 15, 2016 3:19 am
- Forum: OpenMM
- Topic: Monte Carlo and subsets of energy terms
- Replies: 3
- Views: 278
Re: Monte Carlo and subsets of energy terms
I'm also interested in MC simulations where only a subset of energies are calculated. My idea is to use setInteractionGroupParameters() for each MC move, but so far I haven't found a way to do this dynamically during simulation (the context is not updated). Is there a reasonably inexpensive way to d...
- Sat Nov 21, 2015 12:50 am
- Forum: OpenMM
- Topic: dielectric constant for PME/Ewald
- Replies: 4
- Views: 155
Re: dielectric constant for PME/Ewald
Thanks, Peter / Mikael
- Fri Nov 20, 2015 4:06 pm
- Forum: OpenMM
- Topic: dielectric constant for PME/Ewald
- Replies: 4
- Views: 155
Re: dielectric constant for PME/Ewald
Thanks for your help, that is indeed more convenient! I'm implementing the primitive model of electrolytes (albeit with soft spheres) where the pair potential is simply q1*q2/4*pi*eps_0* eps_r *r + LJ, where eps_r is the relative dielectric constant. See here for a jupyter notebook example where Ewa...
- Fri Nov 20, 2015 7:09 am
- Forum: OpenMM
- Topic: dielectric constant for PME/Ewald
- Replies: 4
- Views: 155
dielectric constant for PME/Ewald
I am running CG models in implicit solvent and do not need the solvation terms from GBSA. Is there a way to specify the relative dielectric constant or Bjerrum length for the PME/Ewald methods? Scaling the charges by 1/sqrt(80.) in the xml file works, but seems somewhat cumbersome.