extract force acting on atom A from interactions with atom B

Lee-Ping Wang · Post by **Lee-Ping Wang** » Fri Mar 14, 2014 3:45 am

If you'd like to use ForceBalance please download the latest source code, as I haven't formally released the code in a while (I really should).

https://github.com/leeping/forcebalance

Thanks,

- Lee-Ping

Maciej Dziubinski · Post by **Maciej Dziubinski** » Fri Mar 14, 2014 3:55 am

I'm not familiar with Gaussian. How can I convert a .mol2 or a .pdb file to this .com format?
Also, am I supposed to ask questions like this in the "ForceBalance : Automatic Optimization of Force Fields and Empirical Potentials Public Forum":
https://simtk.org/forums/viewtopic.php? ... 3223#p7140
or start a new topic?

Lee-Ping Wang · Post by **Lee-Ping Wang** » Fri Mar 14, 2014 6:04 am

I'm happy to answer questions anywhere, they all go to my email inbox. If the conversation becomes focused on ForceBalance maybe it's best to use the other forum.

What are you trying to do at the moment? ForceBalance has a script to create force field .itp files starting from Gaussian .com files - I wrote that script because GaussView is an easy way to build molecules (it writes .com files). You might not need that bit for optimizing force fields though.

The overall work flow is to set up a force field file, build a data set and then run the optimization. I can help you along the process.

Maciej Dziubinski · Post by **Maciej Dziubinski** » Mon Mar 17, 2014 1:54 am

OK, ForceBalance works like a charm, but at the moment I only had time to check the 001_water_tutorial.

I have a different project and I was wondering if I could ForceBalance for a quite different purpose than the one we were discussing so far.
I'll ask a few questions without thoroughly reading the doc:
1. Can I use ForceBalance to parameterize pair interactions between (any) two groups of atoms?
2. My system is quite large (~1000 atoms), and the two groups of atoms I'm considering both consist of 5 amino-acid residues. Also, my full atom trajectory is long (say, 10^6 snapshots). Would that be palpable for ForceBalance?

Have I overinterpreted the features of ForceBalance, or am I still in the scope of potential usage?

Lee-Ping Wang · Post by **Lee-Ping Wang** » Tue Mar 18, 2014 1:25 am

Glad the code worked.

Since some of these questions are about ForceBalance, I started a new post over at the ForceBalance forum. The short answer is that your calculation hasn't been attempted in ForceBalance before, though it shouldn't be outside its scope of applicability.

https://simtk.org/forums/viewtopic.php?f=710&t=4754

extract force acting on atom A from interactions with atom B

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