Hope you're enjoying the week! I have some questions about how CHARMM-GUI adds pore waters. I attach the input file below. My questions are:
1) In "Step3: Dynamics", what was the Langevin Dynamics designed for?
2) In "Step3: Dynamics", CHARMM-GUI adds a series of MMFP restraints to waters. Can anyone explain the logic of them?
3) In "Step3: Dynamics", why does the script use a temperature of 5000.0 K for Langevin dynamics?
4) What was "Step3: Individual Comparison" designed for?
Thanks in advance.
Last edited by shane yue; 03/25/14 05:16 PM.