Dear Peter,
That makes sense to me! Thank you so much for your help!!
Best,
Xinyu
Search found 7 matches
- Mon Oct 25, 2021 8:18 pm
- Forum: OpenMM
- Topic: Periodicity of Bond Forces
- Replies: 9
- Views: 422
- Sat Oct 23, 2021 8:35 pm
- Forum: OpenMM
- Topic: Periodicity of Bond Forces
- Replies: 9
- Views: 422
Re: Periodicity of Bond Forces
Dear Peter, This clarification is very helpful to me. Many thanks! By the way, I have another question about the Periodicity of Bond Forces. I have a CustomBondForce which is used for calculating a collective variable between two diffenent molecules. Then I used that collective variable as a reactio...
- Sat Aug 15, 2020 6:15 pm
- Forum: OpenMM
- Topic: How to superpose structures first before calculating the potential?
- Replies: 5
- Views: 139
Re: How to superpose structures first before calculating the potential?
Dear Peter, Thank you very much for your reply. And yes, your understanding is correct. I know it's complicated and I have no idea about how to compute the transformation matrix in an openmm force field - I didn't find a way to read the coordinates of a whole structure during openmm simulation. I wa...
- Fri Aug 14, 2020 4:19 pm
- Forum: OpenMM
- Topic: How to superpose structures first before calculating the potential?
- Replies: 5
- Views: 139
Re: How to superpose structures first before calculating the potential?
Dear Peter, Thank you so much for your quick reply. I'd love to use mdtraj but I'm wondering how to use it in a force field function - I'm writing a cartesian principal component biased potential, like V=k*(pc-pc0)^2. But I need to superpose structures when computing "pc" for each structure during t...
- Fri Aug 14, 2020 3:53 pm
- Forum: OpenMM
- Topic: How to superpose structures first before calculating the potential?
- Replies: 5
- Views: 139
How to superpose structures first before calculating the potential?
Dear all, Hope you all are doing well! I'm wondering if there is a way to superpose structures first before calculating a specific potential. I have a reference structure and I'd like to superpose structures to it and then use the superposed coordinates to calculate a certain potential. Your helps a...
- Thu Jun 06, 2019 12:03 pm
- Forum: OpenMM
- Topic: Setup PBC box
- Replies: 2
- Views: 171
Re: Setup PBC box
Thank you so much for your quick reply! It's pretty helpful!
- Thu Jun 06, 2019 9:35 am
- Forum: OpenMM
- Topic: Setup PBC box
- Replies: 2
- Views: 171
Setup PBC box
Dear OpenMM developers: I'm setting up a simulation with PBC, and find that there are two functions for defining the periodic box: topology.setPeriodicBoxVectors() and system.setDefaultPeriodicBoxVectors(). I'm wondering which one should be chosen and what's their differences? I'll really appreciate...