This just means that SAMSON was not able to get the name of the GPU but it should have detected it properly. Does SAMSON work properly for you or you experience some problems with graphics?
Dear Sudhir, calculation time depends on the exhaustiveness (the higher the slower, but the more exhaustive the search is), the number of rotatable bonds in the ligands (each rotatable bond adds a search dimension) and the number of cores on your computer (the module takes all cores minus one, so your computer remains responsive). This seems normal.
Hello Emmanuel! We were actually talking about you just a few hours ago because we saw your posts about your VR class! It's awesome!
You can actually already move molecules with one hand if you use the "Move" mode (which moves stuff) instead of the "Navigate" mode (which moves yourself).
We decided to use both hands for navigation because we wanted the user to be able to scale as well as rotate / translate the view (7 degrees of freedom), and our tests have shown that this is what is familiar to many people (who use two fingers for scaling on phones). Using both hands and spreading arms / bringing arms closer changes your scale relatively to the molecules. When you move both hands without changing the distance between them you can rotate, translate, etc. Changing the scale in an intuitive way was really important to us to address many different scales as in the virus demo. In the frame below, the user height is around 0.1 microns:
while in this frame (inside the virus) the user height is about 1 nanometer:
(sorry for the video compression blur).
To move molecules instead of yourself, you use the thumbpad in "Move mode" (the two other thumbpad modes are "Add" and "Erase"), and you choose the selection filter that corresponds to what you want to move. This way, you can move a molecule with a single hand (or two molecules with two hands).
For example, in the Selection menu, choose the selection filter called "Structural models" as in the figure below:
Depending on your structures, you might want to select other levels (e.g. molecules, chains, etc., or the default "atoms and bonds").
Then, using the thumbpad, you can rotate / translate when you press on the thumbpad. This is demonstrated e.g. in this video where the user manipulates two carbon nanotubes at the same time to stick them together during interactive simulation. Each hand independently moves each nanotube.
You can have different modes in each hand (e.g. Add on the left hand, Move on the right hand, etc.).
I hope this helps. I'll be happy to talk more about it, as well as about extensions and applications.
To save only the last frame in the trajectory into a PDB file, you can select a path corresponding to this trajectory and set the step to the last one in the Inspector (click Ctrl/Cmd + I to open the Inspector in SAMSON), this will update the structural model - it will correspond to the step you chose. Now you can select the structural model in the Document view and save only the selection as a PDB file, for that in the menu go to Selection > Save selection as and select the PDB format in the types of files.
As for now, there is no direct way to save a .gro file from within SAMSON.
The GROMACS Wizard Element saves the temporary files, including some gro files in a specific scratch folder in your user's directory, the path is different for different OS (Windows, Linux, Mac OS). You can either try looking for the Scratch/GROMACS on your system or check out the path to SAMSON's scratch folder by launching SAMSON-Core-Console executable version and checking for a line with SBGPath::getScratchPath() in the beginning of the console output. On Windows it will be something like: C:\Users\user\AppData\Local\OneAngstrom\SAMSON\DATA\0.8.3\Scratch.
To simulate a protein-membrane complex you can use the GROMACS Wizard Element, using this Element you can easily prepare your system for GROMACS simulation, minimize and equilibrate the structure, and simulate your system using GROMACS. See the GROMACS Wizard tutorial for more information.
Thanks for the link but I tried this too. I does not work all the time. But as I mentioned in YASARA structure, parameterization is a childs' play. How they do it is secret for me but it is kool.
If there will be something like that in SAMSON too, it will be very easy to run complex simulation affectively.
Actually interactive fitting only VMD is providing and that is also very limited. VMD chops off your actual EM map according to the provided pdb model instead of fitting it into the density.
So, as I want to fit multiple structures in the map, I can not do it. I was trying to fit my multi-chain PDB in the same map but it failed.
Chimera do not provide interactive fitting and it fits the protein poorly in the map. Therefore, it is hard to get a proper knowledge of the conformation of any of these tools.
Rest tools are more programming centric, making them hard to be used by biologists having limited programming skills like me.
In the 1st case, you have more functionality and control over processes. The 2nd one is faster to develop and try, and you can further use the developed scripts for your tasks.
For the simulation in which you are interested in, you can use GROMACS Wizard Element (see the GROMACS Wizard tutorial), which allows you to easily run simulations using GROMACS (it comes with the Element) including various temperature ranges. There is yet no possibility to run simulations automatically, but you can launch many simulations in a queue using jobs. In future releases, it will be possible to run them on the cloud. You can freely try this Element for 30-days.
The size of the system for simulation is limited by your computer performance (RAM, CPU, GPU) and the max computation time you are willing to spend. In SAMSON it is possible to load systems with tens of thousands of atoms (depending on the performance of your computer).