-
I am using spam to calculate free energies for a mixed solvent MD simulation (protein is ABL kinase)
My input file is as follows:
parm /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3…
-
While we ask you to address all of the points raised, the following points need to be substantially worked on:
- [x] Consider the missing references pointed out by Referees 2 and 3 (see below).
- …
-
I just wanted to start what will probably be a longer term discussion about storage models.
We should start out by sketching out the data we want to store, as well as the desiderata for our storage m…
-
I assume this problem occurs because utils.Mol2File is applied on my input, a pdb, instead of a mol2 file. Should the ligand always passed as mol2 file?
```
2016-11-22 17:11:51,492: MPI disabled.
…
-
# Upcoming development items
This issue is for **summarising the next couple of steps in the development** for providing all fine-grained functionalities required by a complete integration into the…
-
Hi,
I am trying to find out which of the GIST columns are referenced to bulk water in order to compute the free energy. AMBER tutorial 25 suggests to compute the free energy from all the *-dens co…
-
1 - Plotting free energy estimation seems to me a huge deltaG(target temp=302K), ~5000. Is it as a result from method or is it just a statistical estimation?
2 - I couldn't to reproduce the PMF g…
wever updated
7 years ago
-
**Submitting author:** @qiangyicheng (Yicheng Qiang)
**Repository:** https://github.com/qiangyicheng/flory
**Branch with paper.md** (empty if default branch):
**Version:** 0.2.0
**Editor:** @srmnitc
…
-
Dear CASM developers,
Wondering if vibrational entropy is or being considered in the CASM package right now? If not, what could be the best way to incorporate it under the CASM framework?
Thanks…
-
@jchodera I was trying to run hydration free energy calculation of phenol. I would like to input Yank by using openmm files of the serialized systems (vacuum and solvated phases). I made a .yaml scrip…