How and with what program can I calculate the MD simulation of the proteins modified by polyGlu-tails of different lengths. Will suitable the Gromaks to solve such problem? Thanks for the help!
Hiqmet Kamberaj
If you already have a 3D structure of your protein, then any of these codes, charmm, namd, gromacs, desmond, and maybe others, can be used as MD engine for your simulations. These programs are popular for simulations in water + ion solvents of proteins using different statistical ensembles and constraints.
They also provide many modules to analyse the produced data.
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