Search found 5 matches
- Tue Nov 09, 2021 1:39 am
- Forum: OpenMM
- Topic: understanding openMM minimization, equilibration and production
- Replies: 3
- Views: 476
Re: understanding openMM minimization, equilibration and production
So in the example I posted, openMM would use Langevin Dynamics and minimize until the default values for minimizeEnergy() are reached? Or does it ignore the Langevin integrator and use a default energy minimization algorithm? I might "just" have a problem with the terminology... I cannot find online...
- Mon Nov 08, 2021 7:14 am
- Forum: OpenMM
- Topic: understanding openMM minimization, equilibration and production
- Replies: 3
- Views: 476
understanding openMM minimization, equilibration and production
I have recently switched to openMM coming from GROMACS for simulations of proteins and ligands in explicit solvent . In GROMACS, energy minimization, equilibration and production parameters are stored and read in ".mdp"-files, for example: Energy minimization: ; LINES STARTING WITH ';' ARE COMMENTS ...
- Wed Mar 31, 2021 2:23 am
- Forum: OpenMM
- Topic: python module "openforcefield" for small molecule residue template generators
- Replies: 5
- Views: 786
Re: python module "openforcefield" for small molecule residue template generators
Thanks for this, now the package is loading properly. I am now trying to figure out how to properly create a forcefield object for my new molecule and store it as sdf or xml. It appears I am using the SMIRNOFFTemplateGenerator wrong, or simply use the wrong name for the forcefield I want (amber ff14...
- Mon Mar 29, 2021 1:04 am
- Forum: OpenMM
- Topic: python module "openforcefield" for small molecule residue template generators
- Replies: 5
- Views: 786
Re: python module "openforcefield" for small molecule residue template generators
Thank you, Peter, for catching the embarrassing typos! Installation of the openmmforcefields package has now been successfull, but my python script still fails with the same error: python ThDP_creation.py Traceback (most recent call last): File "ThDP_creation.py", line 2, in <module> from openforcef...
- Fri Mar 26, 2021 1:00 am
- Forum: OpenMM
- Topic: python module "openforcefield" for small molecule residue template generators
- Replies: 5
- Views: 786
python module "openforcefield" for small molecule residue template generators
Dear OpenMM team, I am a first time user of openMM, trying to use the "small residue template generator", as described in section "3.6.3.1. Small molecule residue template generators" of the tutorial here: http://docs.openmm.org/latest/userguide/application.html#small-molecule-residue-template-gener...