Re: [DIYbio] Molecular Dynamics

Interesting program though and cool idea. Current usability just seems limited to making cool gifs.

On Tuesday, October 30, 2012 10:25:56 PM UTC-5, Josiah Zayner wrote:

I was looking at that earlier today but there is not much detailed technical information on it the program.

The screen shot of the simulation tab doesn't even allow someone to change parameters. Temperature? What thermostat are you using?

When you run those simulations is there water? Vacuum? GROMACS 3.3 is very outdated especially if you are using the gmx forcefield. 

What simulation parameters? NVT? NPT? What is your electrostatics cutoff? Are you using PME? 

Are you running solvent restrained dynamics before your production run?

The pictures look great and all but it appears you are only applying forces to atoms to make them move that way? Or am I missing something?

The constructions also don't appear to be chemically relevant i.e. you just place random atoms next to each other without any care for charge or interaction.

Yellow is usually used to represent sulfur, why is it so heavily used in the designs? 

How long are the simulations in nanoseconds? 

On Tuesday, October 30, 2012 9:57:15 PM UTC-5, Bryan Bishop wrote:

On Tue, Oct 30, 2012 at 9:53 PM, Josiah Zayner <josiah...@gmail.com> wrote:

I know it can be a little complex starting out but it seems like an easy and great way for people in DIY Bio to contribute to science. Not just from computational power because there is lots of that but from a intellectual standpoint. Simulating stuff others don't or simulating stuff looking for interesting things.

There's some molecular dynamics stuff here:

https://github.com/kanzure/nanoengineer#readme

- Bryan
http://heybryan.org/
1 512 203 0507

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