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OpenMD

OpenMD is an open source molecular dynamics engine which is capable of efficiently simulating liquids, proteins, nanoparticles, interfaces, and other complex systems using atom types with orientational degrees of freedom (e.g. sticky atoms, point dipoles, and coarse-grained assemblies). Proteins, zeolites, … Continue reading

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Rating: 5.0. From 1 vote.
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Posted in Molecular Dynamics | Leave a comment

xeo

xeo is a free (GPL) open project management for nanostructures using Java Find xeo at: http://sourceforge.net/projects/xeo

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Rating: 4.8. From 4 votes.
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Posted in Chemical Information | Leave a comment

GAMESS

The General Atomic and Molecular Electronic Structure System is a freely availible general ab initio quantum chemistry package. Free graphics programs are also availible for downloading. Find GAMESS at: http://www.msg.ameslab.gov/GAMESS/GAMESS.html

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Rating: 4.6. From 92 votes.
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Posted in Ab Initio Quantum Chemistry | Leave a comment

GROMACS

GROMACS is a very fast molecular dynamics code, which comes with lots of features like PME, a variety of cut-offs, non-equilibrium MD and more. The package includes also other algorithms like normal mode analysis and essential dynamics plus a wealth … Continue reading

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Rating: 4.6. From 78 votes.
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Posted in Molecular Dynamics | Leave a comment

PROCHECK

Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. Find PROCHECK at: https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/

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Rating: 4.5. From 2 votes.
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Posted in Biophysical | Leave a comment

DomainFinder

a free interactive program for the determination and characterization of dynamical domains in proteins. Find DomainFinder at: http://dirac.cnrs-orleans.fr/DomainFinder/

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Rating: 4.5. From 2 votes.
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Posted in Biophysical | Leave a comment

MOSCITO

Moscito is designed for condensed phase and gas phase MD simulations of molecular aggregates. Standard molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS can be employed. Simulations can be carried out in different ensembles such as NVE, NVT … Continue reading

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Rating: 4.4. From 23 votes.
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Posted in Molecular Dynamics | Leave a comment

Gabedit

Gabedit is a graphical interface to Gaussian, Molcas and Molpro computational chemistry packages running locally or on a remote server. It includes a 3D molecule editor and viewer. Most major molecular file formats are supported and graphics can be exported … Continue reading

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Rating: 4.3. From 96 votes.
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Posted in Chemistry | Leave a comment

PGOPHER

PGOPHER is a general purpose program for simulating and fitting rotational spectra. PGOPHER will handle linear molecules and symmetric and asymmetric tops, including effects due to unpaired electrons and nuclear spin. The program can handle many sorts of transitions, including … Continue reading

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Rating: 4.3. From 24 votes.
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Posted in Spectroscopy | Leave a comment

ORAC

ORAC is a program for running classical simulations of biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles. Find ORAC at: http://www.chim.unifi.it/orac/

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Rating: 4.3. From 13 votes.
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Posted in Molecular Dynamics | Leave a comment