-
Hi all, we'd like to use the CD input files to run YANK calculations. In particular, we'd like to start from the `.mol2` files currently in the `nieldev` branch to prepare our solvation boxes in TIP4P…
-
When the DNA library is overly short, Is it possible that most reads overlap.
Can `fastp` stitch these reads together (instead of just correcting errors) ?
So input R1, R2 would produce output R…
-
[GROMACS tutorial](http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html )
[GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design](https://doi.org/10.1021/acs.jcim.2c0004…
-
```
Adding an nrexcl like option to the mapping file would be nice to avoid the
need to create phantom bonds to model the same exclusions as gromacs.
Also see issue #161 for details.
```
Original i…
-
I'm trying to use the orbitals from one SCF as the guess for computations on similar structures. I'm trying to follow this procedure: [https://psicode.org/psi4manual/master/scf.html#restarting-the-scf…
-
A DF-MP3 calculation of C36H38/cc-pVDZ (36ene) fails with a segfault in the OCC module. See attached output file.
[output.txt](https://github.com/psi4/psi4/files/3913671/output.txt)
-
Hi,
Running
```
$ python -m mordred.tests
```
yields an error:
```
======================================================================
FAIL: mordred.tests.test_mordred_main.test_sd…
-
I'm trying to run
mdpow-equilibrium --solvent octanol glyh101.yml
I did the same with --solvent water and had no issues.
I copied the runinput.yml from the templates and made a few changes (copi…
-
**Description**
Consider starting from GROMACS files of something containing a fixed three-site water model. These files include sufficient information to construct a chemical graph that includes i…
-
I'm trying to use your library to design a laser cutter and it would be really helpful if I could add "connectors" to parts and then call a function to connect them together. Basically something like …