Heidi Klem

Heidi Klem
Colorado State University | CSU · Department of Chemistry

About

6
Publications
1,173
Reads
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13
Citations
Citations since 2016
6 Research Items
13 Citations
201620172018201920202021202202468
201620172018201920202021202202468
201620172018201920202021202202468
201620172018201920202021202202468

Publications

Publications (6)
Article
Full-text available
Greater understanding of enzymatic mechanisms aids the discovery of new targets for biologics, the development of biocatalytic transformations, and de novo enzyme design. Methods using quantum mechanical (QM) potentials, such as density functional theory, have enabled complex multistep enzymatic mechanisms to be studied, often in quantitative detai...
Preprint
Determining the optimal number and identity of structural clusters from an ensemble of molecular configurations continues to be a challenge. A common approach is to use a combination of unsupervised dimensionality reduction and subsequent clustering on a large set of internal coordinates followed by kinetic clustering. Here, we present an alternati...
Article
The long-ranged coupling between residues that gives rise to allostery in a protein is built up from short-ranged physical interactions. Computational tools used to predict this coupling and its functional relevance have relied on the application of graph theoretical metrics to residue-level correlations measured from all-atom molecular dynamics (a...
Preprint
Full-text available
The long-ranged coupling between sites that gives rise to allostery in a protein is built up from short-ranged physical interactions. Computational tools used to predict this coupling and its functional relevance have relied heavily on the application of graph theoretical metrics to residue-level correlations measured from all-atom molecular dynami...

Questions

Question (1)
Question
I've been searching for an answer to this question for years, and I'm shocked I haven't found any discussion on any forums. Here is an example to provide more details:
I am preparing a 450 residue protein for simulation. I use tleap to solvate a rectangular box with a 12 Å buffer. > solvatebox mol TIP3PBOX 12
After adding the explicit waters, tleap reports that the volume is 707367.032 Å^3 and the density is 0.833 g/mL, rather than an expected 0.998 g/mL.
It seems that the density is always around 0.85 g/mL.
Therefore I have two questions:
1.) Why does tleap do this?
and
2.) How do you work around this? Right now, my personal workflow is to calculate a corrected volume (i.e., what would the volume need to be to have a 0.998 g/mL density) and use that value to calculate how many ions to add in order to reach my desired ionic concentration for simulation. Then during my equilibrium process of the simulation I allow the box volume to adjust. In the end, during production runs the density is accurate, therefore this problem does not impact my analyses, however it still annoys me.
Thanks for you input!

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