Generating Nanotubes and Running MD Simulations with Gromacs

[Josh]

can this generate topology files for use with Gromacs?

[Bruce Allen]

Hi Josh,

The short answer is no, not directly. You can draw molecules in NanoEngineer-1 and export 

them to Protein databank file format. Do you know if Gromacs supports reading PDB files for its topology content?

You would have to modify NanoEngineer-1 software to read and write native Gromacs topology files. 

NanoEngineer-1  reads and writes its native molecular machine part (MMP) file format. It also 

imports and exports many file types  by means of the Open Babel software built inside NanoEngineer-1. 

Keep in mind, the version of Open Babel is relatively old in 2021 compared to when it was integrated into 

NanoEngineer-1 in 2005-2007. If a recent version of Open Babel supports Gromac, then it would have to be 

reintegrated into  NanoEngineer-1. NanoEngineer-1 is written in Python 2.4-2.6 depending upon the version. 

The current version of Python is 3.8. Python has lots of upgrade issues in regard to its addin packages, which will require

significant changes to its source code. 

My changes to NanoEngineer-1 were to support LAMMPS. 

I do hope you find a solution, 

-bruce

On Wed, Oct 20, 2021 at 8:36 AM Josh <jssant...@gmail.com> wrote:

can this generate topology files for use with Gromacs?

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[Tom]

There is a work around for this.

1. Model your carbon nanotube.

2. Minimize the energy. Select "GROMACS with the ND1 forcefield"

3. NE1 will write all the necessary GROMACS files to some place like:  Minimize All: GROMACS files at C:/Users/Tom/Nanorex/SimFiles\Untitled-minimize-pid13032."

Tom

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[Bruce Allen]

BRAVO!

I never had the opportunity to run that feature in NE-1. I thought it only used the Gromacs force field. 

Thank you!

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[Josh]

Thank you! So there's no need to link NE1 with a current installation of gromacs?

[Josh]

Also it seems like the wiki is lost. Do we have an archive we can refer to? 

So far I'm able to use Nanoengineer in linux based from this github https://github.com/kanzure/nanoengineer albeit I can't make some functions work properly. May I know where I can find a copy of the 2008 release? 

Thank you!

[Tom]

I don't know of another available source for the wiki. If you have specific questions you can ask here. I spent lots of time reading and writing the wiki. Here is a link to download NanoEngineer-1_Suite_v1.1.1.14.exe for anyone that wants it.

https://drive.google.com/file/d/1qocfsi84H_fXhns-cZsYsd667ldM1Zhf/view?usp=sharing

Tom

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