Skip to main content
SpringerLink
Log in

Python Interactive GUI for CHARMM Software Package

  • Chapter
  • First Online:
Computer Simulations in Molecular Biology

Part of the book series: Scientific Computation ((SCIENTCOMP))

  • 279 Accesses

Abstract

In this chapter, we will briefly describe a Python interactive graphical user interface (GUI) for CHARMM package for performing MD simulations of a biological molecular system and standard analysis of in silico data produced from the simulations.

The chapter aims to describe a Python Interactive Graphical User Interface for CHARMM software package.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Source of data: www.charmm.org.

References

  • B.R. Brooks, C.L. Brooks, A.D. MacKerell, L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schaefer, B. Tidor, R.M. Venable, H.L. Woodcock, X. Wu, W. Yang, D.M. York, M. Karplus, Charmm: the bimolecular simulation program. J. Comput. Chem. 30(10), 1545–1614 (2009)

    Article  Google Scholar 

  • W. Humphrey, A. Dalke, K. Schulten, VMD-visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996)

    Article  Google Scholar 

  • H. Kamberaj, Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence. J. Chem. Phys. 143, 124105–8 (2015)

    Article  ADS  Google Scholar 

  • H. Kamberaj, Faster protein folding using enhanced conformational sampling of molecular dynamics simulation. J. Mol. Graph. Model. 81, 32–49 (2018)

    Article  Google Scholar 

  • H. Kamberaj, Heat flow random walks in biomolecular systems using symbolic transfer entropy and graph theory. J. Mol. Graph. Model. 104, 107838 (2021)

    Article  Google Scholar 

  • H. Kamberaj, A. van der Vaart, Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water. J. Chem. Phys. 127, 234102–234109 (2007)

    Article  ADS  Google Scholar 

  • H. Kamberaj, A. van der Vaart, Extracting the causality of correlated motions from molecular dynamic simulations. Biophys. J. 97, 1747–1755 (2009)

    Article  ADS  Google Scholar 

  • D. Nebiu, H. Kamberaj, Symbolic information flow measurement (SIFM): a software for measurement of information flow using symbolic analysis. SoftwareX 11, 100470 (2020)

    Article  Google Scholar 

  • D.V. Schroeder, Interactive molecular dynamics. Am. J. Phys. 83(3), 210–219 (2015)

    Article  ADS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Computer Engineering, International Balkan University, Skopje, North Macedonia

    Hiqmet Kamberaj

Authors
  1. Hiqmet Kamberaj
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hiqmet Kamberaj .

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Kamberaj, H. (2023). Python Interactive GUI for CHARMM Software Package. In: Computer Simulations in Molecular Biology. Scientific Computation. Springer, Cham. https://doi.org/10.1007/978-3-031-34839-6_9

Download citation

Publish with us

Policies and ethics

Search

Navigation