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Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

We recently reported that molecular dynamics simulations for hemoglobin require a surprisingly large box size to stabilize the T(0) state relative to R(0), as observed in experiments (El Hage et al., 2018). Gapsys and de Groot have commented on this work but do not provide convincing evidence that t...

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Detalles Bibliográficos
Autores principales: El Hage, Krystel, Hédin, Florent, Gupta, Prashant K, Meuwly, Markus, Karplus, Martin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586459/
https://www.ncbi.nlm.nih.gov/pubmed/31219783
http://dx.doi.org/10.7554/eLife.45318
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author El Hage, Krystel
Hédin, Florent
Gupta, Prashant K
Meuwly, Markus
Karplus, Martin
author_facet El Hage, Krystel
Hédin, Florent
Gupta, Prashant K
Meuwly, Markus
Karplus, Martin
author_sort El Hage, Krystel
collection PubMed
description We recently reported that molecular dynamics simulations for hemoglobin require a surprisingly large box size to stabilize the T(0) state relative to R(0), as observed in experiments (El Hage et al., 2018). Gapsys and de Groot have commented on this work but do not provide convincing evidence that the conclusions of El Hage et al., 2018 are incorrect. Here we respond to these concerns, argue that our original conclusions remain valid, and raise our own concerns about some of the results reported in the comment by Gapsys and de Groot that require clarification.
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spelling pubmed-65864592019-06-21 Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size' El Hage, Krystel Hédin, Florent Gupta, Prashant K Meuwly, Markus Karplus, Martin eLife Computational and Systems Biology We recently reported that molecular dynamics simulations for hemoglobin require a surprisingly large box size to stabilize the T(0) state relative to R(0), as observed in experiments (El Hage et al., 2018). Gapsys and de Groot have commented on this work but do not provide convincing evidence that the conclusions of El Hage et al., 2018 are incorrect. Here we respond to these concerns, argue that our original conclusions remain valid, and raise our own concerns about some of the results reported in the comment by Gapsys and de Groot that require clarification. eLife Sciences Publications, Ltd 2019-06-20 /pmc/articles/PMC6586459/ /pubmed/31219783 http://dx.doi.org/10.7554/eLife.45318 Text en © 2019, El Hage et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Computational and Systems Biology
El Hage, Krystel
Hédin, Florent
Gupta, Prashant K
Meuwly, Markus
Karplus, Martin
Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_full Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_fullStr Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_full_unstemmed Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_short Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_sort response to comment on 'valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
topic Computational and Systems Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586459/
https://www.ncbi.nlm.nih.gov/pubmed/31219783
http://dx.doi.org/10.7554/eLife.45318
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