Gros Windows Install GROMACS On

Press question mark to learn the rest of the keyboard shortcuts Log In Sign Up User account menu 48 Molecular Dynamics Simulation Gromacs Installation (WinLinux) Beginner Tutorial.

A few comments on the content as I watch it: GROMACS is not one of the accurate, that depends on the forcefield you use (and the way you set up the simulation).

Gros Windows Install GROMACS On

GROMACS runs also on Raspberry Pi by the way, just very slowly:) Saying you install GROMACS on Windows, using the WSL is cheating isnt it:) You might as well say if you are on Windows, get Ubuntu on the WSL and then you have the same commands as in a pure Linux system.

You dont need all those apt-get command if you just do apt-get install gromacs.

All those dependencies (build-essential, etc) are only necessary if you want to compile GROMACS from source, which you would want to do to get the best performance out of your machine (the instructions are on the website you show in the background).

You are better off putting the data in home and run it from there.

Why are you installing GROMACS from APT and then installing it from source PLEASE PLEASE PLEASE DO NOT USE WORDWORDPAD TO EDIT PDB FILES You can use pdb-tools to extract chains very easily on the command line.

You need the -ignh flag to ignore the hydrogen atoms in the file, which usually have different nomenclatures from those in the force field.

You should use this nearly all the time, even with crystallography structures.

Unless you have a complete structure of that particular chain (and even if you do), you should cap your termini so you dont have charged groups that might give you artificial interactions and dynamics.

For those interested in learning more about MD simulations, there are plenty of very good written tutorials out there that you can simply copy paste commands from, or read to learn what each of the them means.

Two examples below: 2 Share Report Save level 1 6 months ago How is this different from PyMOL, which seems easier to set up and use 1 Share Report Save level 2 6 months ago I think you cannot run molecular dynamic simulations with pymol.

Share Report Save level 2 6 months ago Pymol is really just a visualization platform (although it can edit structures you might also be able to build them too).

GROMACS is a molecular dynamics engine used to run simulations.

Share Report Save level 1 6 months ago You should probably be doing this only on ECC RAM machines (servers, HPCs).

To do simulations on a laptop is simply not a good idea - errors in calculation which can bias the simulation.

Share Report Save level 2 6 months ago If you are using a molecular mechanics forcefield, non-bonded distance cutoffs, a timestep large enough to simulate for a decent timescale and a stochastic thermostat then this kind of error is a tiny drop in the ocean of error.

In some ways I wish this was more of a problem, because it means we would have nailed all the algorithmic stuff.

But currently the accuracy of MD is forcefield limited over everything else.

Share Report Save Continue this thread level 2 6 months ago Why would errors creep in on a laptop and not on a cluster Works perfectly well on a laptop as far as I can tell.

Really depends on what one wants to do.

Share Report Save Continue this thread level 2 6 months ago But chemists call simulations bioinformatics (incorrectly).

Share Report Save level 2 PhD Academia 6 months ago Not just relevant anymore: Cells and biochemistry are much more than just nucleic acids.

Also, every single structure of any nucleic acid or protein that you see on the PDB comes from what you call comp chem software.

That reductionism view is first of all quite pessimistic and second of all, just plain wrong, sorry.

Besides, most comp chem people are chemists by training.

Share Report Save Continue this thread level 2 6 months ago these are all complementary disciplines.

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Gromacs Install Windows