[gmx-users] steered molecular dynamics

Mouri Ahmed mouriahmedmou at gmail.com
Sat Nov 12 05:57:08 CET 2016


I would like to run steered molecular dynamics (SMD) in my protein complex
system to find out the PMF without using umbrella sampling.

In the tutorial:after equilibration, the steps are: (a) Generating
Configurations: pull code are used, configurations files are generated, (b)
umbrella sampling.

I am confused about the pull code: pull_coord1_type = umbrella. Will I use
"pull_coord1_type= constant-force" in the mdp file?

After getting the cofigurations file, how will I find the PMF without using
umbrella sampling?

Thanks in advance for the help.

Best Regards

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