OS X nanoengineer download link

[Tim Potter]

Is there a mac installation that is still available for download?  Does anyone know of a download link or a torrent?

[Bruce Allen]

Hi Tim,

This link will take you to my MDS site. You can download the OS X version from there.

http://sourceforge.net/projects/moleculardynami/files/NanoEngineer/

Cheers,

-bruce

On Thu, Apr 30, 2015 at 7:01 PM, Tim Potter <thetim...@gmail.com> wrote:

Is there a mac installation that is still available for download?  Does anyone know of a download link or a torrent?

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[Bruce Allen]

Look at my molecular dynamice studio source forge site. Its in the archive and 2016 directories. It is a smg file.

On Apr 30, 2015 7:01 PM, "Tim Potter" <thetim...@gmail.com> wrote:

Is there a mac installation that is still available for download?  Does anyone know of a download link or a torrent?

--

[Tom]

Thanks, Bruce.

I will check it out. Compared to gromacs, I know almost nothing about LAMMPS. I know NE1 had some rudimentary gromacs integration already. Why did you choose to focus on LAMMPS?  I am reading some LAMMPS vs GROMACS threads now. What are your views?

Tom

[Bruce Allen]

Hi,

I picked LAMMPS because someone at skool was using TINKER and my Prof wanted a more complex tool :)

I also picked LAMMPS because there is an army of guys at Sandia National Laboratory who maintain it and are interested

in metal and polymer systems. GROMACS I would use in a second if I were doing biology. Also, my systems of interest are atomistic. This may change if I have to use large atom counts. There are many people in the Materials Studio, Scienomics and Materials Design communities who also use LAMMPS. 

With that said, I can't offer any truly technical or scientific insights such as LAMMPS will simulate some physical phenomena better than GROMACS. They all are very dependent on 

1. initial model construction <= my area of interest. I am working on a crosslinker

2. force field <== we have no electrons in MD

3. equilibration of the system so the force field actually applies

I am a firm believer in picking the best tool for the job and if you get multiple tools in the same realm of physics

use both and compare the results. I know that Materials Studio has a cryptic table in their force fields where it substitutes 

parameters when a bond, angle, dihedral or OOP can't be satisfied by the highest level of theory. Is this really better than using zeros? The table is called auto_equivalences.

Not much science in this, but I employ what I call the "red face test" I work to build models with 

the correct densities, and moduli prior to doing the actual MD science on the material. I noticed Avogadro will generate

a LAMMPS input file. I would like to integrate NanoEngineer-1, Packmol, MSI2LMP at some point in the future to

have a suite of open source for everyone that wants to do MD, but does not have the cash for the expensive tools. 

-bruce 

  

[Tom]

Hi Bruce,

That is very interesting and honest. Thank you. I am really interested in what you want to use the tools for; what are your systems of interest?  I've attached an image of a 20 million atom system. Say you could model something like that, what would you do?

(please keep the image to yourself)

Tom

[Bruce Allen]

Hi Tom,

Thanks for the feedback. I'm obviously not trying to put companies out of business. They have thousands of man-hours in their products. I'm currently researching polydimethylsiloxane (PDMS) systems at DU. I'm interested in the diffusion of what is known as low molecular weight (LMW) material. These are short chain PDMS molecules. I want to characterize the diffusion times for chains in the 2 to 100 "mer" length since it is felt they contribute to the hydrophobicity of the PDMS surface by constant diffusion. I'm also doing some laboratory work to better understand the depolymerization of PDMS in the environment to understand the rate of depolymerization. There are a couple of mechanisms that could explain this. Molecular Dynamics can't handle reactions, but it can handle the diffusion of the reactions. I'm not sure of the atom counts I need for my diffusion simulations, but more atoms do get me closer to a system that avoid large pressure fluctuations. (66 million atoms is the magic number according to some - I don't have the source name on hand.) Of course building cross-linked systems is important to this modeling since PDMS is well above glass transition temperature and requires the cross-linking as one would see in hardened RTV materials. They also contain fillers as well.  I am also interested in building software that allows the automation of building cross-linked amorphous systems as well. I have an idea I'm working on using the packmol software.  

Finally, building the model and running the simulation are two different things. I have been working with ~3,000 atoms on a i7 870 2.93 GHz iMac with 32GB of RAM. The simulation begs for a large government type cluster and/or GPU(s). With 20 million atoms getting as close to equilibrium during construction has to be important.

I will not show the model (pic)  to anyone, and it is impressive. 

-bruce

[Tom]

Thanks, Bruce.

If I can help produce some larger model files, please let me know. I could send xyz or even mmp. I feel for your need of computer resources. I am in the same boat. :)

Tom

[Bruce Allen]

Hi Tom,

I'm about to spend some cash on a 18 core XEON system and I might get a Titan-Z since it's the same hardware as the more expensive GPUs used for MD. They both have double precision.

This would give me a good platform for my 100,000 mer systems. I have looked at @Xi and Puget Systems.

-bruce

[Tom]

Nice. I've been looking at Puget Systems for a while, but have not ponied up the cash for anything yet. That is one advantage of LAMMPS then over GROMACS. Gmx does not support double precision with GPUs yet that I am aware of.

Tom

[Bruce Allen]

I'll let you know how my new system works out. I'm buying v4 XEON and I want to see how they compare to the 32 v2 XEON cores I have at school. I'm going to run the pice tag past me wife this coming week.

[Tom]

Hi Bruce,

I think we finally figured out the problem with building the NE1 simulator. Details below. Are you still working on NE1/LAMMPS at all? I've been collaborating with guy on interactive molecular dynamics. The first video is steering a C60 with the keyboard and predefined targets which works fairly well. The second is a video of me calibrating a Geomagic Touch haptic device which does not work at all yet.


https://drive.google.com/open?id=0B77-7sY-crCkdExQc1ZyWUpzLUE

https://drive.google.com/open?id=0B77-7sY-crCkcnA3Tk0xaVpTOTg

---from another conversation---

I've finally managed to install the simulator.
Quick-adjust & minimize energy feature in NE-1 briefly tested - works :)

1) I needed to add a linker-flag:
LDFLAGS+=-Wl,--no-as-needed
... to the Unix-section in the Makefile at:
nanoengineeruser@ws034ol:~/nanoengineer-chroot/home/nanoengineeruser/code/nanoengineer/sim/src$

2) make pyx needs to be executed as nanoengieeruser - took a while for me to realize that
(Otherwise I think incompatible/missing python stuff in the host system is tried to be accessed.
-> Misleading Numeric/arrayobject.h not found message)


Am 2016-12-14 um 10:07 schrieb Matt Moses:

Hi Guys,

I do not know if this will be useful to you or not, but here are my notes for setting up Nanoengineer, and also compiling and setting up the "simulator" portion that allows the "adjust" feature to work. Hope it helps! -Matt

//////////////////////////////////////////////////

Notes on Setting up Nanoengineer

The install files are from this link:

https://groups.google.com/forum/#!topic/nanoengineer-dev/SKP6kpH4H0E 

Setting up the Python portion

Once you have the file nanoengineer-chroot.tar.gz, move it to a sensible directory, such as your home directory. Extract it with:

matt@mypc:~$ tar -xvf nanoengineer-chroot.tar.gz

The following needs to be done to set things up every time you run nanoengineer (or at least once after every reboot... i think):

matt@mypc:~$ cd /home/matt/nanoengineer-chroot/

matt@mypc:~/nanoengineer-chroot$ sudo mount -t proc none proc

[sudo] password for matt: ************

matt@mypc:~/nanoengineer-chroot$ sudo mount -o bind /tmp tmp

You can run these commands to check that ubuntu's graphics stuff is working properly. Some of these may need mesa-utils to be installed. If you don't have it, install with sudo apt-get install mesa-utils.

matt@mypc:~/nanoengineer-chroot$ echo $DISPLAY

:0

matt@mypc:~/nanoengineer-chroot$ xeyes

(xeyes should open a window showing a little pair of cartoon eyes...)

matt@mypc:~/nanoengineer-chroot$ glxgears

(glxgears should open a window with animated gears...)

If all that checks out, try running nanoengineer:

matt@mypc:~/nanoengineer-chroot$ sudo chroot /home/matt/nanoengineer-chroot/

root@mypc:/# su nanoengineeruser (the password is 'password')

nanoengineeruser@mypc:/$ python /home/nanoengineeruser/code/nanoengineer/cad/src/main.py

///////////////////////////////////////////////

Notes on Compiling and Installing the Simulator

Now we build the sim.so file (The technical name for this is apparently a 'shared library extension module'). This executable is used by the python CAD code for energy minimization. First cd to the directory:

nanoengineeruser@mypc:/$ cd code/nanoengineer/sim/src

nanoengineeruser@mypc:~/code/nanoengineer/sim/src$

OK, we're dropping the long text in front of the prompt, but you stay in the same directory.

$ make clean

$ make

$ touch *.pyx

$ make clean

$ make pyx

Now if you look for modified files like this

$ ls -altr

one of the latest files should be "sim.so". That's the one we want. Now cd up and over to cad:

$ cd ../../cad

You should now be in /home/nanoengineeruser/code/nanoengineer/cad

You need to make the bin directory:

$ mkdir bin

and then lastly you need to copy over the sim.so file you just made: 

$ cp ../sim/src/sim.so ./bin

Now you should be able to cd to home and start Nanoengineer the normal way:

$ cd ~

$ python /home/nanoengineeruser/code/nanoengineer/cad/src/main.py

and "Adjust" and "Minimize" should work, as long as minimize is set to use ND1 only and not Gromacs.

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[Bruce Allen]

Hi Tom,

I'm mostly working on my PhD.  I need to work more on MDS software too.

I have been sick or injured since late October as well.

Thank you for a wealth of information!

-bruce

[nisha kumari]

Hii 

pls provide link to download nanoengineer on mac and guide too how it can be installed .

Thanks

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[Tom]

I only have a Windows installer here. https://drive.google.com/file/d/1qocfsi84H_fXhns-cZsYsd667ldM1Zhf/view?usp=sharing

Tom

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[Bruce Allen]

Hi Tom,

How can i help? 

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[Bruce Allen]

Here is the link to the OSX. This is a dmg file and you just point at it to do the install on OSX from what I remember.

https://sourceforge.net/projects/moleculardynami/files/2016Release/NanoEngineer/executable/osx/

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[nyzar elmheiri]

Thank you.

‫في الثلاثاء، 8 مارس 2022 في 6:11 ص تمت كتابة ما يلي بواسطة ‪Bruce Allen‬‏ <‪balle...@gmail.com‬‏>:‬

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[Bruce Allen]

You are welcome

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