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Molecular Dynamics
Jump to new posts Re: cluster analysis by rmv @ 04/28/17 12:17 PM

As Lennart noted, clustering dihedrals and distances at the same time can be tricky. I'm not convinced that dividing by the fluctuations is the correct choice, esp. for the dihedrals. I would leave the dihedrals alone, since the clustering code und
Jump to new posts Use Amber FF with CHARMM-GUI output? by abrol @ 04/26/17 09:33 PM

Hi, Is there a way to use the CHARMM-GUI output in AMBER format with AMBER FF? The default appears to be the C36 FF. Thanks, Ravi
Performance and Benchmarking
Jump to new posts Re: Correct implementation of OpenMM by lennart @ 04/25/17 09:29 AM

gbsw is not supported with OpenMM
Jump to new posts Question regarding GCMC/BD Ion Simulator by Carlos Navarro @ 04/24/17 09:07 PM

Dear all, I'm trying to set up a system to estimate ion fluxes. For that I set up the system with all defaults values from charmm-gui ion simulator module. By using pb-pnp I created all three .bin files, but when using gcmc.bd_rfpar I got the followi