list of software that uses GromacsWrapper

[orbeckst]

For the paper #147 it would be very beneficial to demonstrate that GromacsWrapper has been used elsewhere, especially in software or work that can be cited.

Please add to this issue any citation for work that used GromacsWrapper.

[orbeckst]

@AndySomogyi didn't you use GW for your multiscale code?

[orbeckst]

We used GromacsWrapper for the MDPOW workflow in

1. O. Beckstein, A. Fourrier, and B. I. Iorga. Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field. J Comput Aided Mol Des, 28(3):265–276, 2014.
2. O. Beckstein and B. I. Iorga. Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the opls-aa force field. J Comput Aided Mol Des, 26(5):635–645, 2012.
3. I. M. Kenney, O. Beckstein, and B. I. Iorga. Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field. J Comput Aided Mol Des, 30(11):1045–1058, 2016.

[orbeckst]

@dotsdl did you use GW for any of your published papers? Or only for mdworks?

[jandom]

Aye – will get to it as soon as i return from my well-deserved holiday trip to the remote ends of the Carpathian Mountains ⛰ (which will be in 1 week)

On Mon, Aug 27, 2018 at 9:59 AM Oliver Beckstein [email protected] wrote:

@dotsdl https://github.com/dotsdl did you use GW for any of your published papers? Or only for mdworks https://github.com/Becksteinlab/mdworks?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/Becksteinlab/GromacsWrapper/issues/163#issuecomment-416147241, or mute the thread https://github.com/notifications/unsubscribe-auth/AAYKm_mNlBrv7LLcP1l1lGU8tDp7y8Eaks5uU6bngaJpZM4WNWCr .

[pslacerda]

The group that I belong at UFBA/Salvador (or used to because now I'm really on the internet industry) was mostly a pharmaceutical (and biotech) group. Python data structures and error handling is generally too much computing for most of us. Even the software I made wasn't really used by them.

[whitead]

1. Combining Enhanced Sampling with Experiment Directed Simulation of the GYG peptide. DB Amirkulova, AD White. (2018) Journal of Theoretical Computational Chemistry. 17 (03): 1840007.
2. Encoding and Selecting Coarse-Grain MappingOperators in Hierarchical Graphs. C Maghesree, C Xu, AD White. (2018) Submitted (available on arxiv)

[PicoCentauri]

We currently have a paper in review where I used GromacsWrapper

Philip Loche, Cihan Ayaz, Alexander Schlaich, Douwe J. Bonthuis, and Roland R. Netz. Breakdown of linear dielectric theory for the interaction between hydrated ions and graphene. Physical Chemistry Letters, 2018.