=== This is the readme file ===
=== September 8, 2016 =========
The partial charges are calculated correctly after all!
I did find the following problem:
The nmsi2lmp does not add the 0.5A offset for the MD cell in all XYZ space.
This was fixed.
Also, was able to compare identical models one in a CAR/MDF file format with
an MMP file format. They both generated identical LAMMPS Geometry Input Files (LGIF).
The MD cell boundary problem may have caused lost atoms during simulation.
=== August 4, 2016 ============
I have more problems with calculation of the atom partial charges.
I am working to get this fixed this weekend. This appears to be a problem
since the original alpha release.
=== August 2, 2016 ============
I have recently regression tested the three software applications that compose MDS.
I took an old DGEBA/IPD system and read it with NanaoEngineer-1.
I then wrote the new MMP file containing both numeric atom types and the industry standard
alphanumeric atom types.
I then created a 5 oligomer system using packmol to verify all atom types are passed through
to the new system MMP file.
I then created a LAMMPS Geomoetry Input File using msi2lmp.
I noticed many missing nonbonded parameters so I used the nonbond equvilances to
manually enter pairs of parameters into the CFF91.frc file I use.
I did noticed that my previous software in the achive missed generating the Angle-Angle
parameters for a C-C-N-H geometry. This is generated now.
Of course this is just one simulation but it appears to generate the desired system density.
The LAMMPS run shrunk the system from 60A per-side of a MD cell to 32A per-side.
=== July 25, 2016 =============
The LAMMPS file generated by MSI2LMP needs your attention!
The file has the following changes:
1. READ THE RELEASE NOTE THAT COME WITH LAMMPS in the tools section.
2. MMP files and NanoEngineer-1 does not yet support triclinic geometries for the MD cell
3. I fixed the dimensions for the rectangular prisim box so the tool writes out the correct dimension.
4. I will explore the support the triclinic as soon as I can.
The new Windows msi2lmp.exe is not available. OSX and Linux to soon follow.
=== July 23, 2016 =============
Working on tracking down bugs in all MDS applications.
I'm sorry for
On windows is the msi2lmp and not the nmis2lmp.
I need to fix problems with it.
=== July 19, 2016 =============
I will be working on updating Packmol to the latest and greatest version soon.
I have a newer version below, but not as new as Dr. Martinez's latest release.
I have recently secured Intel FORTRAN compiler for OSX and Linux as well as C/C++ compiler for Linux
because I am developing this website and modifications to integrate the 3 software components.
I have added the Linux version of packmol to the 2016 release.
Make sure to use the syntax ./packmol file.inp to run this version of packmol.
=== July 19, 2016 =============
I have added the OSX version of packmol to the 2016 release.
Make sure to use the syntax ./packmol file.inp to run this version of packmol.
I'm working on a Linux version.
=== July 11, 2016 =============
I have added the most up to date version of msi2lmp to the 2016 release for Windows, OSX and Linux.
The following should be kept in mind:
1. msi2lmp source has to be modified to turn off the strick checking for force field parameters or
the program exits when the first missing parameter case occurs. This is just the opposite of
historical msi2lmp behavior.
2. Read the README that is in the LAMMPS msi2lmp to understand all the new features and forcefields supported.
3. The $BIOSYM_LIBRARY environment variable has been replaced with $MSI2LMP_LIBRARY.
Windows executable: nmsi2lmp.exe
OSX executable: msi2lmp.exe
Linux executable: msi2lmp.exe
=== July, 8 2016 ==============
I have added a new ZIP file called Windows Release. This has all the programs you need along
with the cff91 force field.
I just want to point out the following:
1. User NanoEngineer-1 to draw molecules. You can draw one or one million molecules. Put
a single molecule in a single MMP file. Now you want to build a system of molecules to simulate.
2. Use PACKMOL to create a system of molecules. PACKMOL will pack a defined volume with any
number of molecules you prescribe in the *.inp file per MOLECULE you prescribe. You could
build a system of 1000 water molecules and 1000 urea molecules. You only have to draw water and
urea molecules once! PACMOL does the rest!!!
3. Now run MSI2LMP on the final MMP file generated by PACKMOL! This gives you a LAMMPS Geometry
Input File (LGIF) for your final LAMMPS simulation!
=== July 2, 2016 ==============
The Windows versions of the NanoEngineer-1, PACKMOL and MSI2LMP are available for use. Please
report tickets for problems. The source for the NanoEngineer-1 changes still needs to be uploaded.
The advance here is to use alphanumerical atomtypes. This means that force fields cff91 and unpulblished
COMPASS can be used since NanoEngineer-1 uses them. Addional changes coming will include additional force fields
and all numerical atomtypes will be gone.
=== June 30, 2016 =============
1. The NanoEngineer-1 tool depends on grabing compiled Python modules from library.zip in the Windows environment
The new and/or modified modules are placed in this library. The library.zip is a ZIP file with one special twist,
this file is a STORE file and the STORE feature must be selected in your compression tool. I bought two licenses
of WINWAR a few month back because it is such an excellent tool! By right clicking on the library.zip file and
going to properties you can see the Archive tab. Select the Archive tab and the graphic should show the version as
1.0 and the Host OS as DOS. If you see version 2.0 the ZIP file was zipped incorrectly and can be extracted and
re-ZIPPED. A 100% Ratio is necessary for NanoEngineer-1 to use the ZIP file.
2. Just as important, you must create the achive so the directories in the library directory are at the top of
the library.zip file.
=== June 29, 2016 =============
The following changes will take effect by July 15th, 2016
Changes are in progress for Molecular Dynamics Studio
NanoEngineer-1 has been modified to use alphanumeric atomtypes. Going forward the new version of the software will save the numerical
and alphanumerical atom types to the Molecular Machine Part File (MMP). Alphanumerical atomtypes are the atomtypes used in the standard
force field files. The whole purpose of moving to alphanumeric atomtypes is to make use of them in the MSi2LMP tool. No more modifications
of the force field files will be necessary.
The latest version of Packmol has been modified to pass the alphanumerica atomtypes through from the MMP file templates to the final
MMP system file created my Packmol. This will allow modified version MSI2LMP to use the alphanumeric atomtypes directly as stated above.
The latest version of MSi2LMP has been modifed to parse the new MMP file format containing alphanumeric atomtypes. It reads in the
bond increments from the force field file to calculate partial atom charges for the LAMMPS full atom model.
TESTING OF THE ABOVE NEW FUNCTIONALITY IS GOING WELL.
The following changes will take effect by Sept 30th, 2016
This applies to atomistic force fields.
NanoEngineer-1 will dynamically manage force fields. The user will designate a directory via an environment variable, which will
contain all the *.frc files they have from whatever source. NanoEngineer-1 will upon startup open the directory, grab the file names, and
read in all the alphanumerica atom types along with descriptions. Next it will create dictionaries of buttons for the atomtypes and the
entries in the spin button so the user can select whatever force field they want.
This will create an MMP file BUT you might need to do some backend work on MSI2LMP if the force field is not CFF.
=== July 4th 2015 =============
I built a windows 7 x64 version of Packmol that has my MMP file modifcations in it.
PACKMOL => Windows_x64 => Windows_x64_packmol_w_mmp.exe
Just rename the executable so it's easier to use.
MAKE SURE TO RUN THIS VERSION AS FOLLOWS:
C:\mix packmol.exe mixturemmpb.inp
This assumes you renamed the executable to packmol.exe
This assumes you named your input file mixturemmpb.inp
DON"T USED THE "<" UNIX "goes into" symbol!
=== June 16 2015 ==============
After buying the Intel FORTRAN compiler for Visual Studio, I hope to build versions of Packmol for
the Windows platform - x86 and x64.
I have added a Windows-x64 version of the ORIGINAL Packmol here as a test. I will add one of my modified
=== I have replaced the msi2lmp individual file downloads with a tar file and I have done the same for the packmol modifications. The documentation for building the software
=== was updated as well. Please contact me when something is not working and I will respond as soon as I can.
=== Thank you!
=== I HAVE UPLOADED THE CORRECT COPY OF LIBRARY.ZIP. I HAVE HAD THE INCORRECT COPY ON THE SITE SINCE THE BEGINNING. PLEASE DOWNLOAD THE CORRECT COPY
=== THE NANOENGINEER-1 WITH THE CFF91 FORCE FIELD SHOULD WORK AS EXPECTED.
=== NOTE: Nanoengineer-1.net has been down for a while and the owner has gotten it back up!
You can download NanoEngineer-1 for Windows, MAC and Linux from this site. My changes only apply to the Windows version of the software - for now.
=== FOR THE TIME BEING PLEASE DOWNLOAD THE msi2lmp.tar.gz FILE IF YOU WANT TO BUILD ON CYGWIN AND PERHAPS LINUX. IF YOU WANT TO BUILD UNDER
=== WINDOWS JUST CREATE A PROJECT FILE AND USE THE SOURCE CODE TO BUILD AN EXECUTABLE. ONCE YOU HAVE THE msi2lmp executable you can
=== name it ne2lmp so it is different from the msi2lmp executable. AT THIS POINT IN TIME I WILL CONSTRUCT AN ne2lmp executable so it is a seperate
=== Apparently the MSI2LMP tool is still being maintained!!! I have to determine if I can submit my changes for inclusion into
=== the existing code base or just create a new tool from the source I started with.
=== Modifying the current baseline of MSI2LMP with my changes will require more work than copying my changed and new files over top
=== of the current baseline, which could change over time.
=== I apologize for not providing the global.i file earlier for the PACKMOL modifications!!! This will allow the changes to compile and link.
It has come to my attention that there could be a problem with registering at the NANOREX, Inc. website to download the
original NanoEngineer-1. This is needed to apply the library.zip file to. I am uploading the file since I registered
a long time ago on the site. My changes only apply, for now, to the Windows version. I am also supplying the source code
and the MAC versions of the application. I will be working to make my modifications work on MAC and Linux as time goes on.
I am sorry this is a problem.
=== IT IS IMPORTANT TO NOTE THAT THE THREE SOFTWARE APPLICATIONS ARE USED IN A SERIAL MANNER.
===1. ONE CREATE TEMPLATES OF MOLECULES USING NANOENGINEER-1. YOU WILL HAVE ONE OR MORE MOLECULAR MACHINE PART FILES
=== (mmp) EACH WITH A SEPERATE MOLECULE. DON'T FORGET TO MINIMIZE ITS ENERGY.
===2. CREATE THE *.INP FILE FOR PACKMOL. THE EXAMPLES DIRECTORY NOW CONTAINS EXAMPLES OF AN OLIGOMER AND WATER
=== AND A *.INP FILE FOR PACKMOL - E.G. SQUARECFF91.INP. BY RUNNING WITH THE *.INP FILE YOU CAN CREATE THE DGEBAWATER.MMP FILE.
=== PLEASE SEE THE EXAMPLES.
===3. RUN THE MSI2LMP TO CONVERT DGEBAWATER.MMP INTO A LAMMPS GEOMETRY INPUT FILE. THIS PROCESS REQUIRES THE NUMERIC CFF91
=== FILE IN THE NUMERIC CFF91 DIRECTORY. THIS REQUIRES SETTING UP THE BIOSYM_LIBRARY ENVIRONMENT VARIABLE UNDER YOUR OPERATING SYSTEM.
=== THE cff91_cff91v.frc file MUST BE IN THE DIRECTORY YOU POINT TO WITH THIS ENVIRONMENT VARIABLE.
=== I HAVE SEEN MANY DOWNLOADS AND WOULD LIKE VERY MUCH TO HEAR BACK ABOUT PROBLEMS AND ISSUES
=== PLEASE RESPOND THROUGH THE SOURCE FORGE SITE AND I WILL RESPOND VIA GMAIL
=== gmail: claudevms AT gmail DOT com
=== 9/9/2012 - Resumed uploading source files for this project ===
=== 9/12/2012 -MODIFIED README FILE
===10/04/2012 -ADDED THE MSI2LMP.EXE file for WINDOWS. This was build using VC++ in VS 2008
=== -MSI2LMP.EXE converts the MMP file from either NE-1 or the modified PACKMOL into
=== a LAMMPS Geometry Input File. You must use the force field file located in the NUMERIC
=== CFF91 directory. Please download and read the directions of MSI2LMP in the LAMMPS distribution
=== to setup the environment variables!!!
===10/04/2012 -ADDED an example file to the EXAMPLES directory. square3cff91.mmp is a molecular machine part file
=== I created by hand in NE-1. It is a cross-linked oligomer consisting of 4 IPD molecules and 9 DGEBA
=== molecules. The configuration of the oligomer was shamlessly borrowed from Tack & Ford who
=== developed this configuration for their MD simulations.
===10/04/2012 -ADDED suggestion on how to run PACKMOL on Windows using the CYGWIN/MING build executable.
===10/04/2012 -ADDED CYGWIN PACKMOL executable to the Windows executables directory including the CYGWIN
=== the DLLs needed for the Windows system directory. I suggest installing CYGWIN and trying out a
=== fantastic and masterful work of opensource!!! I put the DLLs in here really to provide the names
===10/10/2012 I APOLOGIZE FOR SPECIFYING SERVICE PACK 1 FOR WINDOWS 7. THERE IS A DLL ISSUE WITH SP1 AND YOU
=== CANNOT RUN THE MODIFIED NANOENGINEER-1 UNDER SP1!!!
===10/10/2012 I HAVE DISCOVERED RECENTLY THAT THE NANOENGINEER-1 WIKI SITE IS DOWN. THIS SITE IS CRITICAL TO
=== TO CREATING A DEVELOPMENT VERSION OF THE NANOENGINEER-1 SOFTWARE AND RUNNING IT INSIDE WINGIDE.
===10/10/2012 I'M WORKING ON TWO PDF DOCUMENTS ONE IS A BUILD AND INSTALLATION AND THE SECOND IS A SCIENCE DOCUMENT
=== EXPLAINING HOW TO BUILD AN MD CELL AND THE LAMMPS SIMULATIONS USED TO CALCULATE DENSITY AND GLASS
=== TRANSITION TEMPERATURE
===10/12/2012 I have added a draft Build and Installation PDF to the documentation directory
===10/12/2012 I have updated my slides for my master's defense and uploaded it to show the initial operational capability (IOC) of
=== Molecular Dynamics Studio
===10/16/2012 Added PACMOL input files squarecff91.mmp and water.mmp. Added squarecff91.inp, which is the PACMOL command file
=== if you place all files in a common directory you can run packmol at the command line packmol squarecff91.inp
=== and generate the dgebawater.mmp file. You can use NanoEngineer-1 to look at the final system containing 5 oligomers and
=== 20 water molecules. The dgebawater.mmp in in the PACKMOL out files directory.
===10/17/2012 Added very draft software instructions into the documentation directory
WARNING: I BELIEVE ALL FILES HAVE BEEN UPLOADED!!! YOU MUST DOWNLOAD ALL FILES FOR
NANOENGINEER-1, PACKMOL AND MSI2LMP INORDER TO EFFECTIVELY USE THE SOFTWARE.
PLEASE SUBMIT TROUBLE TICKETS OR EMAIL ME AND I WILL RESPOND WITH FIXES AS I CAN.
NOTE: THE SOFTWARE DOES NOT CONTAIN ANY COMPASS FORCE FIELD INFORMATION. THE PROJECT STARTED
USING THE PUBLISHED COMPASS FORCEFIELD DATA FROM THE SUN PAPERS. ONCE IT WAS DETERMINED THAT COMPASS COULD
NOT BE USED IN ITS ENTIRETY, CFF91 WAS USED. REFERENCES TO COMPASS PUBLISHED AND UNPUBLISHED IN NANOENGINEER-1 ARE
EXAMPLES OF HOW MULTIPLE FORCEFIELDS COULD BE ADDED TO THE SOFTWARE. ANY FORCEFIELD EXISTS AS A COLLECTION
OF ATOM TYPE SYMBOLS WHILE ONE WOULD REQUIRE THE FORCEFIELD FILE FROM THE OWNER. I COULD HAVE REFERENCED
AMBER OR OTHER FORCEFIELDS IN THE SELECTION WIDGET.
NanoEngineer-1 can be downloaded from http://www.nanoengineer-1.com/content/
You must create an account to download NanoEngineer-1 at the Nanorex site
Go to this URL for details: http://www.nanoengineer-1.net/mediawiki/index.php?title=Online_Readme
Once you install NanoEngineer-1 on your Windows XP, Vista or Windows 7 operating system
you must place the library.zip file into the C:\Program File(x86)\Nanorex\NanoEngineer-1v1.1.1\program
directory. First rename the existing library.zip if you want to return to the original software.
PACKMOL can be downloaded from http://www.ime.unicamp.br/~martinez/packmol/
You must copy the modified files into the directory where you install PACKMOL and follow the PACKMOL
build instructions. I created a packmolnew.f file so I could debug the program easierly. It uses > and <
to direct file input output and that conflicts with DDD/gdb. You may want to build PACKMOL
under CYGWIN or MING - I found that easy. NOTE: once you build PACKMOL executable under MING or CYGWIN you can
run it under windows without CYGWIN or MING by adding the following CYGWIN libraries to the Windows
system directory: cygg_s-1.dll, cyggfortran-3.dll cygwin1.dll. The PACKMOL executable will look for these
libraries in order to execute on a plain Windows platform.
MSI2LMP can be downloaded as part of the LAMMPS molecular dynamics software from http://lammps.sandia.gov/
The LAMMPS software is distributed as a tar.gz file. Follow the directions for downloading, decompressing
and untaring the software. A directory is created containing all LAMMPS software. The MSI2LMP software
is located in ../lammps-ddmmmyy/tools/msi2lmp/src. Copy the modified files into the installation directory
above. Save the original files if you need them.
MSI2LMP can be built for UNIX/Linux/OSX or Windows. Building the software for Windows requires creating a
project file in Visual Studio and adding the source to the project. Building for Unix/Linux/OSX requires
running the make for the platform.
Running the software
1. Run NanoEngineer-1 and create indivdual files for all the specific molecules you want to place
in the MD cell. There will be one MMP file per molecule.
2. After reading the PACKMOL user manual create a PACKMOL input file that contains references to
the molecules created in step 1 and the number of each molecules you want in the MD cell. PACKMOL
will create a single MMP file containing the MD cell.
3. Run the MSI2LMP program using the MMP file created by PACKMOL. This creates a LAMMPS geometry input file
ready for simulation.
SAW - self avoiding walk - which is still in development will be a tool to build MD cells using molecule templates created
from templates created in NanoEngineer-1. The software is being developed in C++ and will eventually integrate LAMMPS
via the callable interface. The goal is to have a software tool to support the creation of crosslinking via a dynamic
mechanism where molecules move over time and are "reacted" with one another based on rules the user defines.
More and detailed information is to follow...