Search found 102 matches

by Lee-Ping Wang
Sun Jan 21, 2018 8:15 am
Forum: ForceBalance : Automatic Optimization of Force Fields and Empirical Potentials
Topic: Some trouble with examples
Replies: 4
Views: 470

Re: Some trouble with examples

That's great! Please let me know if you have any more issues.
by Lee-Ping Wang
Wed Jan 17, 2018 11:25 am
Forum: ForceBalance : Automatic Optimization of Force Fields and Empirical Potentials
Topic: Some trouble with examples
Replies: 4
Views: 470

Re: Some trouble with examples

Hello Manuel, Thanks for posting your question. When the liquid bromine example runs, it actually executes a script "rungmx.sh" which then executes a Python script "npt.py". It is important that "rungmx.sh" sets the environment variables correctly so that "npt.py" can import the ForceBalance modules...
by Lee-Ping Wang
Fri Jul 08, 2016 7:21 pm
Forum: ForceBalance : Automatic Optimization of Force Fields and Empirical Potentials
Topic: Residue mismatch with ForceField
Replies: 3
Views: 354

Re: Residue mismatch with ForceField

Ah, thanks for coming back with the update. I admit I didn't see your earlier message.

If your changes to the code are useful in a broader context, would you consider contributing it back to the main repository at github.com/leeping/forcebalance ?

Thanks,

- Lee-Ping
by Lee-Ping Wang
Wed Apr 13, 2016 3:40 pm
Forum: OpenMM
Topic: Question about restraining the center of mass
Replies: 2
Views: 271

Re: Question about restraining the center of mass

Thanks a lot. :) That seems a lot simpler than creating a fictitious atom.
by Lee-Ping Wang
Wed Apr 13, 2016 3:16 pm
Forum: OpenMM
Topic: Question about restraining the center of mass
Replies: 2
Views: 271

Question about restraining the center of mass

Hi there, If I wanted to restrain the center of mass of a molecule to a particular position (without restraining the individual atoms), should I use the CustomCentroidBondForce? I could create a fictitious particle with no mass and no other interactions so that it stays at a prescribed position, and...
by Lee-Ping Wang
Tue May 26, 2015 8:45 pm
Forum: ForceBalance : Automatic Optimization of Force Fields and Empirical Potentials
Topic: ForceBalance and Amber
Replies: 6
Views: 742

Re: ForceBalance and Amber

Glad to hear it. Yes, please stay in touch.

- Lee-Ping
by Lee-Ping Wang
Tue May 26, 2015 2:40 pm
Forum: ForceBalance : Automatic Optimization of Force Fields and Empirical Potentials
Topic: ForceBalance and Amber
Replies: 6
Views: 742

Re: ForceBalance and Amber

Ahh, I think I know what's going on. Thanks for the error report. With the current AMBER version, I don't think it correctly loops over the whole trajectory when writing the forces; instead it just writes the first force and quits. Additionally, it prints out the force components (i.e. bond, angle e...
by Lee-Ping Wang
Fri May 22, 2015 1:06 am
Forum: ForceBalance : Automatic Optimization of Force Fields and Empirical Potentials
Topic: ForceBalance and Amber
Replies: 6
Views: 742

Re: ForceBalance and Amber

Hi Isaiah, Thanks for your message. I'm glad you're interested in using ForceBalance. ForceBalance does support AMBER for parameterizing force fields, but it can't convert a GROMACS force field format to AMBER. If you change AbInitio_GMX to AbInitio_AMBER, you also need to change some files in force...
by Lee-Ping Wang
Sun May 03, 2015 4:52 pm
Forum: OpenMM
Topic: OpenMM Tinker Make Error
Replies: 2
Views: 323

Re: OpenMM Tinker Make Error

Hi Sean, I know about this problem, and it comes from a recent (<6 mos.) change to the OpenMM API. You're probably linking against version of OpenMM that is too old, and it doesn't have the API change. Try with the newest development build of OpenMM (git clone https://github.com/pandegroup/openmm) a...
by Lee-Ping Wang
Fri May 01, 2015 12:46 pm
Forum: OpenMM
Topic: Cpu overhead
Replies: 6
Views: 324

Re: Cpu overhead

Hi Peter, I don't know all the nuts and bolts of how common batch systems work (e.g. PBS, SGE, Slurm), but my impression is that they do not place actual restrictions on the number of cores when a user submits a job. It's up to the user to restrict the number of cores that are used. This is distinct...