MDynaMix

{{Infobox software

| name = Molecular Dynamics of Mixtures

| logo =

| logo alt =

| logo caption =

| screenshot = Image:MDynaMix-MGE.png

| screenshot alt = Computer display showing temperature function on left, DNA molecule in center, and various menu items to right and below.

| caption = DNA simulation on MDynaMix

| author = Aatto Laaksonen, Alexander Lyubartsev

| developer = Stockholm University, Department of Materials and Environmental Chemistry, Division of Physical Chemistry

| released = {{Start date and age|1993}}

| latest release version = 5.3.0

| latest release date = {{Start date and age|df=yes|2019|01|15}}{{cite web

| url = http://www.fos.su.se/~sasha/mdynamix/

| title = MDynaMix Homepage

| website = fos.su.se

| access-date = 2021-04-15

}}

| latest preview version =

| latest preview date =

| programming language = Fortran 77-90

| operating system = Unix, Unix-like, Linux, Windows

| platform = x86, x86-64, Cray

| size =

| language = English

| genre = Molecular dynamics

| license = GPL

| website = {{URL|www.fos.su.se/~sasha/mdynamix}}

| repo =

| standard =

| AsOf =

}}

Molecular Dynamics of Mixtures (MDynaMix) is a computer software package for general purpose molecular dynamics to simulate mixtures of molecules, interacting by AMBER- and CHARMM-like force fields in periodic boundary conditions.{{cite journal |doi= 10.1016/S0010-4655(99)00529-9 |title= MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures |author= A.P.Lyubartsev, A.Laaksonen |journal= Computer Physics Communications |volume= 128 |year=2000 |pages= 565–589 |issue= 3|bibcode= 2000CoPhC.128..565L }}{{cite book |title= Applied Parallel Computing Large Scale Scientific and Industrial Problems

|chapter= Parallel molecular dynamics simulations of biomolecular systems

|author= A.P.Lyubartsev, A.Laaksonen |series= Lecture Notes in Computer Science

|isbn= 978-3-540-65414-8 |doi= 10.1007/BFb0095310|s2cid= 26892490

}}

Algorithms are included for NVE, NVT, NPT, anisotropic NPT ensembles, and Ewald summation to treat electrostatic interactions.

The code was written in a mix of Fortran 77 and 90 (with Message Passing Interface (MPI) for parallel execution). The package runs on Unix and Unix-like (Linux) workstations, clusters of workstations, and on Windows in sequential mode.

MDynaMix is developed at the Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Sweden. It is released as open-source software under a GNU General Public License (GPL).

Programs

md is the main MDynaMix block
makemol is a utility which provides help to create files describing molecular structure and the force field
tranal is a suite of utilities to analyze trajectories
mdee is a version of the program which implements expanded ensemble method to compute free energy and chemical potential (is not parallelized)
mge provides a graphical user interface to construct molecular models and monitor dynamics process

Field of application

Thermodynamic properties of liquids{{cite journal

|doi= 10.1039/b108726f

|title= Thermodynamic properties and interfacial tension of a model water–carbon dioxide system

|issue= 6|bibcode= 2002PCCP....4..937K

}}

Nucleic acid - ions interaction{{cite journal

|title= Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study

|pmid= 16449204

|issue= 2

|doi= 10.1093/nar/gkj434

|pmc= 1356527}}

Modeling of lipid bilayers{{cite journal

|title= Modification of the CHARMM force field for DMPC lipid bilayer

|pmid= 18512235

|issue= 14

|doi= 10.1002/jcc.20974|s2cid=8599984 }}

Polyelectrolytes{{cite journal

|title= Specifics of solvation of sulfonated polyelectrolytes in water, dimethylmethylphosphonate, and their mixture: A molecular simulation study

|pmid= 18447495

|issue= 16

|doi= 10.1063/1.2899327|bibcode=2008JChPh.128p4902V |s2cid=948639 }}

Ionic liquids{{cite journal

|title= Thermodynamical and structural properties of imidazolium based ionic liquids from molecular simulation

|pmid= 18433237

|issue= 15

|doi= 10.1063/1.2907332|bibcode=2008JChPh.128o4509R }}{{cite journal

|title= Molecular dynamics simulation of room-temperature ionic liquid mixture of [bmim][BF₄] and acetonitrile by a refined force field

|pmid= 16189592

|issue= 14

|doi= 10.1039/b504681p|bibcode=2005PCCP....7.2771W }}

X-ray spectra of liquid water{{cite journal

|title= Theoretical modeling and interpretation of X-ray absorption spectra of liquid water

|pmid= 17043717

|issue= 41

|doi= 10.1039/b607093k|bibcode=2006PCCP....8.4744W }}

Force Field development{{cite journal

|doi= 10.1002/jcc.20721

|title= A new six-site acetonitrile model for simulations of liquid acetonitril and its aqueous mixture

|issue= 12 |year=2007 |pages=2020–2026

|pmid= 17450554|s2cid= 5333395

}}{{cite journal

|doi= 10.1016/j.chemphys.2007.12.006

|title= Solvation of monovalent anions in formamide and methanol: Parameterization of the IEF-PCM model

|year=2008 |pages=101–113|bibcode= 2008CP....344..101B

}}

References

External links

{{Official website|www.fos.su.se/~sasha/mdynamix}}
[http://biomolecular-modeling.com/Ascalaph/ Ascalaph, graphical shell for MDynaMix] (GNU GPL)

Category:Molecular dynamics software

Category:Free science software

Category:Free software programmed in C++

Category:Free software programmed in Fortran

MDynaMix

Programs

Field of application

See also

References

External links