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We need to integrate existing implementations of DFT-D3 and DFT-TS into the main source.
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For example:
```
db = ChemlabDB()
db.vdw["Li"]
db.masses["H"]
db.vdw.keys()
```
However there could be some problems with online databases (can you list all possible molecules from an online databas…
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Dear Dr. Qifeng Bai,
I work in computational chemistry. I have been using the MOLAICAL code for MMGBSA calculations for NAMD 100ns trajectories, and it has been working greatly, specially with the ne…
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Hi, I am new to this software/tools and stucked at this step while preparing topology files with the following command (attached prot_lig.pdb file for --> "complex"-->protein_ligand.prmtop) for MDS si…
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Hi,
I am new to QuickFF and try to fit a suite parameters for my system. Following by the examples in QuickFF/share/systems, I can get parameters of covalent interactions and electrostatic contrib…
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The `molcularnodes/data.py::elements` dictionary contains information about elements, where the element symbols are keys to access a subdictionary for each element. The subdictionaries have keys such …
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Need a consistent way to address properties in properties.py ... currently some bits are returned as dictionaries some are added to system objects.
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I want to decompose the energies of a system by atom, but am puzzled by the outputs. I'm using commands of the form
energy test1 @2 out test1.txt
energy test2 @1-10 out test2.txt
with the trpzi…
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I am running a molecular dynamics simulation of a single polymer chain in water. I want to calculate the solvent accessible surface area of the polymer over the course of the simulation.
Per the e…
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Respected Sir, I am new user of RASPA, when I am starting a simulation the following error is showing, kindly tell me how to overcome this problem.
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERAC…