[gmx-users] steered molecular dynamics

Mouri Ahmed mouriahmedmou at gmail.com
Sat Nov 12 04:30:39 CET 2016

Hi Sir,

Many thanks for the help. 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?

Best Regards

On Fri, Nov 11, 2016 at 8:34 PM, Nikhil Maroli <scinikhil at gmail.com> wrote:

> What exactly are you looking for ?
> http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_
> Conference_2013/Computing_potentials_of_mean_force%3A_
> Justin_Lemkul,_Session_2A
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