[OUTDATED] Desmond - Analyzing MD Trajectories with the Simulation Interactions Diagram (Part 4)

[@SchrodingerInc]

Please see learn.schrodinger.com/private/edu/release/current/Documentation/html/tutorials/desmond_intro/desmond_intro.htm? for updated steps.

[@李尧慧]

Hi, I am wondering how did this panel do the alignment when using the first frame as the reference structure? Based on CA, backbone, side chain or...? Thanks!

[@fahimalamnobel4789]

How many configurations of pc is needed to do MD? My pc configuration is cori5,4gp ram 1tera rom. And the operating system is windows 10

[@radnukespeoplesminds]

is there a way to do the analysis through command line on linux?

[@ignaciolizana3252]

Can I analyze a NAMD MD trayectory (.dcd) with Desmond?

[@fabriziofierro2419]

Hi! Is it possible to convert a gromacs trajectory file (.xtc) into a .cms file, in order to analyze it with desmond?

[@lamiaelkhattabi9714]

it is possible ????

[@sinhasuman1944]

Hi, very nice video tutorials. Thanks for it. I have following questions: is it possible to do a QM/MM simulation also of a protein-ligand system as easily as demonstrated in these Desmond videos? Also kindly let me know if free energy of binding can be straightway calculated using Desmond.

[@SchrodingerInc]

Hi Sinha Suman, Thanks for your comment. Yes, you can do a QM/MM simulation of protein-ligand systems using Schrödinger's program QSite (www.schrodinger.com/QSite/). We don't currently have any video tutorials for QSite, however, the QSite User Guide contains detailed information including a tutorial. It is available via Maestro or from www.schrodinger.com/supportdocs/ Once opened within Maestro the QSite panel quick help button also contains details on how to set up and use the panel. Best regards, Jarred