These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
229 related articles for article (PubMed ID: 27196035)
1. TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD. Vermaas JV; Hardy DJ; Stone JE; Tajkhorshid E; Kohlmeyer A J Chem Inf Model; 2016 Jun; 56(6):1112-6. PubMed ID: 27196035 [TBL] [Abstract][Full Text] [Related]
2. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Lee J; Cheng X; Swails JM; Yeom MS; Eastman PK; Lemkul JA; Wei S; Buckner J; Jeong JC; Qi Y; Jo S; Pande VS; Case DA; Brooks CL; MacKerell AD; Klauda JB; Im W J Chem Theory Comput; 2016 Jan; 12(1):405-13. PubMed ID: 26631602 [TBL] [Abstract][Full Text] [Related]
3. MDWiZ: a platform for the automated translation of molecular dynamics simulations. Rusu VH; Horta VA; Horta BA; Lins RD; Baron R J Mol Graph Model; 2014 Mar; 48():80-6. PubMed ID: 24434017 [TBL] [Abstract][Full Text] [Related]
4. Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations. Lundborg M; Lindahl E J Phys Chem B; 2015 Jan; 119(3):810-23. PubMed ID: 25343332 [TBL] [Abstract][Full Text] [Related]
5. Combination of the CHARMM27 force field with united-atom lipid force fields. Sapay N; Tieleman DP J Comput Chem; 2011 May; 32(7):1400-10. PubMed ID: 21425293 [TBL] [Abstract][Full Text] [Related]
6. CHARMM-GUI 10 years for biomolecular modeling and simulation. Jo S; Cheng X; Lee J; Kim S; Park SJ; Patel DS; Beaven AH; Lee KI; Rui H; Park S; Lee HS; Roux B; MacKerell AD; Klauda JB; Qi Y; Im W J Comput Chem; 2017 Jun; 38(15):1114-1124. PubMed ID: 27862047 [TBL] [Abstract][Full Text] [Related]
7. CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. Kognole AA; Lee J; Park SJ; Jo S; Chatterjee P; Lemkul JA; Huang J; MacKerell AD; Im W J Comput Chem; 2022 Feb; 43(5):359-375. PubMed ID: 34874077 [TBL] [Abstract][Full Text] [Related]
8. DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields. Bernardes CES J Chem Inf Model; 2022 Mar; 62(6):1471-1478. PubMed ID: 35239343 [TBL] [Abstract][Full Text] [Related]
9. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Shirts MR; Klein C; Swails JM; Yin J; Gilson MK; Mobley DL; Case DA; Zhong ED J Comput Aided Mol Des; 2017 Jan; 31(1):147-161. PubMed ID: 27787702 [TBL] [Abstract][Full Text] [Related]
10. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. Kim S; Lee J; Jo S; Brooks CL; Lee HS; Im W J Comput Chem; 2017 Jun; 38(21):1879-1886. PubMed ID: 28497616 [TBL] [Abstract][Full Text] [Related]
11. charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS. Wacha AF; Lemkul JA J Chem Inf Model; 2023 Jul; 63(14):4246-4252. PubMed ID: 37399236 [TBL] [Abstract][Full Text] [Related]
12. From GROMACS to LAMMPS: GRO2LAM : A converter for molecular dynamics software. Chávez Thielemann H; Cardellini A; Fasano M; Bergamasco L; Alberghini M; Ciorra G; Chiavazzo E; Asinari P J Mol Model; 2019 May; 25(6):147. PubMed ID: 31065808 [TBL] [Abstract][Full Text] [Related]
13. Molecular dynamics simulation by GROMACS using GUI plugin for PyMOL. Makarewicz T; Kaźmierkiewicz R J Chem Inf Model; 2013 May; 53(5):1229-34. PubMed ID: 23611462 [TBL] [Abstract][Full Text] [Related]
14. MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations. Liu H; Jin Y; Ding H Brief Bioinform; 2023 Mar; 24(2):. PubMed ID: 36790845 [TBL] [Abstract][Full Text] [Related]
15. The ACPYPE web server for small-molecule MD topology generation. Kagami L; Wilter A; Diaz A; Vranken W Bioinformatics; 2023 Jun; 39(6):. PubMed ID: 37252824 [TBL] [Abstract][Full Text] [Related]
16. pmx: Automated protein structure and topology generation for alchemical perturbations. Gapsys V; Michielssens S; Seeliger D; de Groot BL J Comput Chem; 2015 Feb; 36(5):348-54. PubMed ID: 25487359 [TBL] [Abstract][Full Text] [Related]
17. pyCHARMM: Embedding CHARMM Functionality in a Python Framework. Buckner J; Liu X; Chakravorty A; Wu Y; Cervantes LF; Lai TT; Brooks CL J Chem Theory Comput; 2023 Jun; 19(12):3752-3762. PubMed ID: 37267404 [TBL] [Abstract][Full Text] [Related]
18. ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines. Chen H; Fu H; Shao X; Chipot C; Cai W J Chem Inf Model; 2018 Jul; 58(7):1315-1318. PubMed ID: 29874076 [TBL] [Abstract][Full Text] [Related]
19. jSimMacs for GROMACS: a Java application for advanced molecular dynamics simulations with remote access capability. Roopra S; Knapp B; Omasits U; Schreiner W J Chem Inf Model; 2009 Oct; 49(10):2412-7. PubMed ID: 19852516 [TBL] [Abstract][Full Text] [Related]
20. Comparison of protein force fields for molecular dynamics simulations. Guvench O; MacKerell AD Methods Mol Biol; 2008; 443():63-88. PubMed ID: 18446282 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]