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Molecule topologies
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This page lists contributed topologies from GROMACS users. They have not been verified or tested by the GROMACS developers.
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| File | Size | Date | Attached by | |
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| |  | 1-1_CHOL-DPPC.zip The zip file contains 43A1-S3 topology for 1:1 cholesterol-DPPC bilayer with an equilibrated box of 256 cholesterols and 256 DPPC lipids as well as 15499 SPCE waters | 2.3 MB | 23:04, 4 Jan 2011 | schiu | | | | | AA_DMPC.tar.gz All-atomistic topology for DMPC. Includes a equilibrated bilayer with 128 lipids and 3840 water molecules. Needs lipids_forcefield.ff.tar.gz. Ref: J. Phys. Chem. B, DOI: 10.1021/jp212503e | 337.42 kB | 16:16, 7 Mar 2012 | joakim? | | | | | AA_DPPC.tar.gz All-atomistic topology for DPPC. Includes a equilibrated bilayer with 128 lipids and 3840 water molecules. Needs lipids_forcefield.ff.tar.gz. Ref: J. Phys. Chem. B, DOI: 10.1021/jp212503e | 357.61 kB | 16:16, 7 Mar 2012 | joakim? | | | | | argon_1000.zip Liquid argon (1000 atoms) with an experimental density equilibrated at 80K (NVT). | 33.77 kB | 10:21, 23 May 2009 | rossen | | | | | azucyt23.pdb.gz Azurin is a small blu copper protein consisting of 128 residue and whit a redox center, a copper ion, that is coordinated by three equatirials ligands: ND HIS 117 , ND HIS 46, SG CYS 112 Uploaded 09:26 September 14, 2004 by Brunori (brunori at unitus.it) | 35.79 kB | 11:05, 23 May 2009 | rossen | | | | | C4mimNTf2.tgz The package contains a topology for the ionic liquid [C4mim][NTf2] published in "T. Köddermann, D.Paschek, R. Ludwig., Chem. Phys. Chem., 8: 2464-2470, 2007" along with a box of 216 ion pairs. | 67.86 kB | 12:44, 18 Nov 2011 | koeddermann? | | | | | ccl4_box.tgz The package contains a topology for opls rigid model CCl4 along with an equilibrated box of 512 molecules and a run input file. Uploaded 16:53 May 20, 2003 by PeiQuan Chen (gromacs@163.com) | 53.5 kB | 11:04, 23 May 2009 | rossen | | | | | ch2cl2_box.tgz The package contains a topology for opls rigid model CH2Cl2 along with an equilibrated box of 512 molecules and a run input file. Uploaded 17:01 May 20, 2003 by PeiQuan Chen (gromacs@163.com) | 32.95 kB | 11:03, 23 May 2009 | rossen | | | | | chcl3_box.tgz The package contains a topology for opls rigid model CHCl3 along with an equilibrated box of 512 molecules and a run input file. Uploaded 16:59 May 20, 2003 by PeiQuan Chen (gromacs@163.com) | 43.25 kB | 11:03, 23 May 2009 | rossen | | | | | cholesterol.tgz This united-atom topology of cholesterol [ C17H22(CH3)2OHC6H11(CH3)2 ] is intended to be used with the normal ffgmx force field. Uploaded April 12, 1999 by Monika Hoeltje (hense@pharm.uni-duesseldorf.de) | 2.67 kB | 11:03, 23 May 2009 | rossen | | | | | DLPC.zip This package consists of 43A1-S3 force field topology for DLPC lipid molecule and an equilibrated box of fluid-phase DLPC bilayers (100 DLPC + 3205 SPCE waters). | 515.75 kB | 23:36, 4 Jan 2011 | schiu | | | | | DMPC.zip This package consists of 43A1-S3 force field topology for DMPC lipid molecule and an equilibrated box of fluid-phase DMPC bilayers (100 DMPC + 3205 SPCE waters). | 532.42 kB | 23:36, 4 Jan 2011 | schiu | | | | | dmso_AL.tgz The package contains a topology for DMSO along with an equilibrated box of 250 molecules and a run input file. Uploaded 13:52 March 13, 2003 by Christoph Freudenberger (christoph.freudenberger@chemie.uni-ulm.de) | 22.72 kB | 10:58, 23 May 2009 | rossen | | | | | DOPC.zip This package consists of 43A1-S3 force field topology for DOPC lipid molecule and an equilibrated box of fluid-phase DOPC bilayers (128 DOPC + 4825 SPCE waters). | 802.71 kB | 23:32, 4 Jan 2011 | schiu | | | | | DPPC.zip This package consists of 43A1-S3 force field topology for DPPC lipid molecule and an equilibrated box of fluid-phase DPPC bilayers (100 DPPC + 3205 SPCE waters). | 542.96 kB | 23:32, 4 Jan 2011 | schiu | | | | | Fe4S4.tar.gz Aps Reductase cofactor Uploaded 14:27 June 13, 2005 by Eliass Silva dos Santos (elias at fis.ufba.br) | 828 bytes | 10:58, 23 May 2009 | rossen | | | | | GDP.tgz This is the GROMOS96(ffG43a1) topology of GDP. No hydrogen is added to the beta-phosphate. Net charge is +3. And the charge are calculated in MMFF94(Sybyl>>Calculte>>Charge>>MMFF94). Note that charge calculated by Gaussian is too large(compared with the GUA in ffG43a1.rtp) and will make the structure deform during MD simulation. The initial topology file is generated by PRODRG. Uploaded 02:58 November 23, 2004 by Zhenting Gao (zhentg at 163.com) | 2.99 kB | 23:37, 13 Jun 2009 | rossen | | | | | GUANIDINE-L.zip This the topology for guanidinium chloride and two boxes with 3M and 5M of gnd in water. The topology is described in C. Camilloni, A. Guerini Rocco, I. Eberini, E. Gianazza, R. A. Broglia, and G. Tiana, Urea and guanidinium chloride denature Protein L in different ways in molecular dynamics simulations, Biophys. J., 98 (2008), DOI: 10.1529/biophysj.107.125799; | 45.81 kB | 10:23, 23 May 2009 | rossen | | | | | heptane_box.tar.gz A heptane solvent box with 20 molecules (using -nbox 5 2 2 in genconf). Uploaded 18:10 June 09, 2003 by Aswin Sai Narain. S (aswin_biogenie@yahoo.co.uk) | 1994 bytes | 10:23, 23 May 2009 | rossen | | | | | LipidsForGro96_53a6.zip Lipid topologies and equilibrated bilayers of DPPC, DMPC, POPC and POPG for the GROMOS96 53a6 force field. The details are published in: Kukol, A (2009), Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins, J Chem Theo Comput, available from http://pubs.acs.org/journal/jctcce, DOI: 10.1021/ct8003468 | 793.7 kB | 10:21, 23 May 2009 | rossen | | | | | Mar278940.tgz Steelink Structure:
GROMOS96 43a or 43b Uploaded 18:46 March 27, 2002 by Tiona Todoruk (trtodoru@ucalgary.ca) | 725.24 kB | 10:15, 23 May 2009 | rossen | | | | | mecn_box.tgz The package contains a topology for MeCN along with an equilibrated box of 300 molecules and a run input file. Uploaded 08:41 March 12, 2003 by Christoph Freudenberger (christoph.freudenberger@chemie.uni-ulm.de) | 32.27 kB | 11:05, 23 May 2009 | rossen | | | | | methanol216.gro.gz equilibrated methanol box at 300K and 1 bar. Uploaded 11:57 December 09, 2002 by Bert de Groot (bgroot@gwdg.de) | 14.02 kB | 10:21, 23 May 2009 | rossen | | | | | methanol_opls.tar.gz equilibrated methanol box (1728 molecules, approx. 5x5x5nm^3) at 298K, 1bar, PME, rlist=1,rcoulomb=1, rvdw=1.4, DispCorr=EnerPres, average density ~770 Uploaded 10:24 January 19, 2004 by Rainer Böckmann (rainer@bioc.unizh.ch) | 133 kB | 10:21, 23 May 2009 | rossen | | | | | methanol_WFG.tgz The package contains a topology for MeOH along with an equilibrated box of 400 molecules and a run input file. Uploaded 13:56 March 13, 2003 by Christoph Freudenberger (christoph.freudenberger@chemie.uni-ulm.de) | 27.25 kB | 10:21, 23 May 2009 | rossen | | | | | octanol.tar.gz The package contains a topology for octanol(oplsaa model) along with an equilibrated box of 512 molecules and a run input file. Uploaded 06:53 February 05, 2004 by PeiQuan Chen (gromacs@163.com) | 307.4 kB | 10:16, 23 May 2009 | rossen | | | | | PGO.tar.gz Propylene glycol molecule developed with ff43a2x (GROMOS96) from 3.1.4 Contains topology file, non-bonding parameters file and coordinate file of 2ns equilibrated box with 1800 molecules DHvap (exp/calc) = 58.0 / 56.7 kJ mol-1 Density (exp/calc) = 1036 / 1035 kg m-3 Uploaded 03:56 October 08, 2003 by Dallas Warren | 267.92 kB | 10:16, 23 May 2009 | rossen | | | | | POPC.zip This package consists of 43A1-S3 force field topology for POPC lipid molecule and an equilibrated box of fluid-phase POPC bilayers (128 POPC + 3552 SPCE waters). | 648.48 kB | 23:32, 4 Jan 2011 | schiu | | | | | SM.zip This package consists of 43A1-S3 force field topology for SM lipid molecule and an equilibrated box of fluid-phase sphingomyelin bilayers (100 SM + 3162 SPCE waters). | 552.78 kB | 23:36, 4 Jan 2011 | schiu | | | | | swcnt+dmso.zip Single-walled carbon nanotube (SWCNT) with a few layers of DMSO molecules inside and outside:
SWCNT(15x15), dCNT=2nm, LCNT=6 nm + 1415 DMSO. Simulated box=(5.0; 5.0; 9.0). The system was additionally equilibrated for 200ps at 300K (md). | 229.81 kB | 10:15, 23 May 2009 | rossen | | | | | U10.tar.gz Ubiquinone 10 is a crucial electron acceptor in the Cytochrome B complex. This molecule has originally 10 isoprene units as a tail, but these have not been included in this model. Uploaded 12:13 September 18, 2001 by Sergio Manzetti (s.manzetti@student.qut.edu.au) | 2.09 kB | 10:15, 23 May 2009 | rossen | |
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