Starting simulations in Win 10



  • Dear all,

    I am new to SAMSON and I am already impressed. It looks amazing!

    I started trying to follow the tutorials.

    First thing I notice is that not all the interaction models used in Tutorials are in my installation (I do not have Brenner, ASED-MO, among others).

    The second thing is that even setting up a simulation with an available simulation model like Lennard-Jones or UFF, and starting using an structure out of equilibrium, after starting the simulation, nothing happens (I do not see any indication that my structure is relaxing).

    What I am doing wrong?

    Regards,

    Camps



  • Dear Camps,

    thank you very much for your interest in SAMSON and the nice compliment! Brenner and ASED-MO are unfortunately not available at the moment.

    After starting interactive simulation (with the Simulation / Start simulation menu, or with the Space bar, or with the corresponding icon 0_1542221216422_play.png) and depending on which state updater you have chosen, you might have to change the step size in order to see some changes in the structure (for example 0.1 instead of 0.01). In many state updaters you can also change the number of steps between two viewport updates (e.g. set this to 10 to refresh the viewport every ten simulation steps).

    Does this help?

    Best,

    Stephane



  • Dear Camps,

    I thought I'd clarify what's going on with Brenner and ASED-MO. While SAMSON and numerous SAMSON Elements are and will remain free forever, both for academia and industry, some SAMSON Elements will now have a commercial license (for industry and / or academia).

    In effect, SAMSON Connect is becoming a marketplace for molecular modeling, where developers have the possibility to integrate and commercialize their tools (think App store for molecular modeling, except everything is integrated into a single, universal platform which makes it possible to combine modules together and gives new possibilities). Our goal is to contribute to the development of an integrated ecosystem for molecular modeling, where users can install tools in a few clicks, have them all integrated in the same platform, are able to combine them, pipeline them, etc. Since SAMSON has an open architecture, and the SAMSON API makes it possible for anyone to integrate existing tools, create new ones from scratch, develop new force fields, create new visualizations, etc., you can imagine the huge possibilities the SAMSON model gives.

    As with other marketplaces (iOS, Android, etc.), many SAMSON Elements are and will continue to be free, and new free SAMSON Elements will continue to be published. However, our goal with this hybrid economic model is to reach the best of both worlds: serve the molecular modeling community while supporting the development of the best possible platform.

    At the moment, anyone can get a free month of some commercial SAMSON Elements (including Brenner) by answering the short survey at https://forms.office.com/Pages/ResponsePage.aspx?id=Cg7MSY8KzkinPF492orBMZM0kpSnVmtKp3madpYYjexUQ0c5V1Q3VUEwVEtHQlhSWVVJRUFGN1lVQy4u.

    At the end of the survey, they can choose which SAMSON Element they want among:

    • Brenner interaction model (interactive simulation for carbon nanotubes, graphene, etc.)
    • Crystal creator (build complex crystals structures)
    • Normal modes advanced (non-linear normal modes analysis for proteins binding sites)

    and we'll add it to their account (registering is and will always be free, and SAMSON itself will always be free).

    Best,

    Stephane


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