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Project Admins:

• Bryan

[Bryan]

As it states in the 'NOTES.txt' that come with the package, v2.0 is currently in beta, so some features are missing from the drop down menus, and any feedback (including bugs) would be appreciated.

[Bryan]

A new release of v2.0 has been uploaded (v2.0.3), it contains a couple of very important bug fixes related to the scaling of the experimental form factors and the chi squared calculation.

It is also the very first version that includes the trajectory reader. This is very much a work in progress, and at the moment can only read 'GRO/XTC' combinations together with MARTINI coarse grained trajectories. I realize this is the least useful for comparing to experimental work, but it was added for future extensions to the software that are more simulation driven. The atomistic and united atom simulations are causing problems at the moment, but should be fixed by the next mini-release.

[Bryan]

Okay, v2.0.4 has been uploaded with what should be a fully functioning trajectory reader, including atomistic simulations. It has been successfully tested on XTC files up to 250 MB in size. There are more details in the notes that come with the download, but a very brief overview:

-> improved trajectory reader, atomistic and MARTINI
-> can now save/load SIMtoEXP formats under 'Export'
-> the trajectory reader allows a fraction (up to all) of the water to be changed to heavy water (D2O).

The 'input' folder comes with both types of trajectories to be used a tests. It should be noted that it is assumed the bilayers have been centered along the normal axis prior to analysis!

The next major release will be the official release of v2, and will include accurate form factors for MARTINI beads.

[Bryan]

My apologies to those who have already downloaded 2.0.4, but there has been a major bug fix so I needed to put out this new mini-release. The bug was only showing up when dealing with large trajectories, but would cause a fatal crash. The problem SHOULD be fixed now (PLEASE let me know if you experience any problems), and the code has been tested on XTC files up to 2.0 GB in size; a couple of other minor bug fixes have also been included.

NOTE: the program no longer automatically trims bulk water from the system, this is left up to the user to export the densities, cut out any portion that is undesirable, and reload the densities. I plan to eventually include a "trim" function so these steps won't be necessary, but for now this is seen as more transparent.

[Bryan]

Can now export the number densities on a "per particle" basis (as well as the previous "elemental"), similar to those used in v1.0. If the user loads this "per particle" file back in, they can now use 'cmp' files to create the component electron and neutron scattering length densities that correspond to the model of interest to the user. There is a sample component file for DAPC in the 'input' folder; this file uses deuterium, so make sure to select some non-zero fraction of deuterium, or simply remove it from the '.cmp' file. Please note the names must match between the '.sim' file and the '.cmp' file, and that the naming matches the (particle/residue) names from the gro file.

The long term plan is to include common component models automatically, but it is unlikely this will be implemented soon.

All of the component exports also work now, but the component number densities can't be loaded back in to SIMtoEXP (the ED and NSLD are fine though), use xmgrace or a similar plotting program to look at these afterword.

For the trajectory reader: a major memory issue has been addressed. The trajectory reader used to use nearly 10x the size of the 'xtc' file in memory, and this clearly limits the size of trajectories that can be used. This has been fixed, with the only tradeoff being the file has to be read twice (the first read is quite fast anyway). The trajectory reader now uses a constant amount of memory < 80 MB, and should be able to handle ANY size 'xtc' file.