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It has become standard practice in the membrane protein simulation world to set up membrane systems using CHARMM-GUI. However, it is not yet common for such labs to then simulate their systems using O…
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Hello professor, I am using your fluctmatch, when executing the run_fm, I entered topology file and trajectory file, but always remind me subprocess. CalledProcessError: Command '['/home/zhaichaoying/…
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Hi, I am new to OpenMM I am trying to simulate alanine dipeptide in water. However,
I am facing the following issues when I use Charmm Forcefield. I am attaching the PDB file and my Python script.
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Hello developer, first of all thank you for your work. I'd like to ask you two questions. First, whether it is possible to parmed the gromacs topology file (.top) into the charmm topology file (.psf),…
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~~Currently, we are reading atom types/names from a CHARMM parameter file,
probably we can make a default list in the GUI and let the user add or change new atom types/names
or even better: make a r…
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I have in mind two possible target systems to use as an example for the membrane barostat:
- DOPC bilayer using the CHARMM force field (all-atom)
- DOPC bilayer using the MARTINI 3 force field (co…
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e.g. CHARMM sterochemistry, anything that uses a list of pairs/triples of particles should all be trivially parallelizable with OpenMP.
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CHARMM PDBs have 3 HIS residues: HSD, HSE ans HSP. These alternative names should be accounted as HIS during reduction
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In `_get_dihedral_types` in `lammpsdata.py`, the weighting factor for CHARMM dihedrals is determined as the reciprocal of the length of the list of dihedral terms for a given dihedral. This is probab…
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The Charmm forcefield includes elements for improper dihedrals (which are supported in OpenMM and ParmEd). Foyer needs to accept CustomTorsionForce elements also