Alex Izvorski

Second order total variation [feature request]

2

I'd like to use second-order total variation, as described in for example these couple of papers: https://www.ipol.im/pub/art/2013/40/article.pdf http://www.franklenzen.de/pdf/lenzen_et_al_ssvm2013.pdf In other words, instead of trying to minimize sum of first derivative...

Use 'quantities' library to handle conversions between simulation units and actual units

13

I'm wondering what the units used for each quantity are, both for parameters which are passed in and for values stored internally or produced by the calculation. A lot of...

How to use yank for peptide-protein binding?

1

I'd like to use yank to calculate binding free energy for a peptide binding to a protein. I couldn't find any examples of this, so I'm not sure if this...

Get gradients at every step during geometry optimization

4

**Is your feature request related to a problem? Please describe.** I'd like to get the gradients for every step during a geometry optimization **Describe the solution you'd like** `xtb input.xyz...

Add all Amber ion params

11

Amber has quite a lot of different kinds of ion parameters in `dat/leap/parm/frcmod.ions*`. There are sets for each water model, which can be either the Li/Merz "lm" or Joung/Cheatham "jc"...

Get particle from atom?

5

I'm wondering if there is any way to relate application-level objects (eg `app.Atom`) to library-level objects (eg particle). For example: ``` for atom in topology.atoms(): atom_index = ??? # index...

Add Amber ff19SB params

7

Reference: https://pubs.acs.org/doi/10.1021/acs.jctc.9b00591 or https://chemrxiv.org/engage/chemrxiv/article-details/60c7426b0f50db0f23395cd7 From the Amber22 manual, "ff19SB [19] is the latest model of the SB protein forcefields, developed in the Simmerling Lab at Stony Brook University. The new...

Read periodic box from pdb file

3

I noticed that PDB files can contain periodic box vectors. For example, if a periodic system is written out from tleap with `savepdb system system.pdb`, it would end up with...

Optimize memory access in computeNonbonded

57

Here is some initial profiling of memory accesses in computeNonbonded using nsight-compute - this is a single execution of the computeNonbonded kernel on the STMV system:  Collected with: `/opt/nvidia/nsight-compute/2021.3.0/ncu...

Changing force group after creating context affects context (different on CPU and CUDA)

11

I was trying to do energy decomposition by changing the force group of one force at a time, getting the energy for that force group only and then changing it...