If you're proceeding blindly, then you're likely going to frustrate yourself to
>no end. There is literature relevant to what you're doing - pulling on
>peptides/proteins to unfold them is something that's been done. So you should
>have some methodological precedent.
>"Non-Protein" is a default group that should have been written to the .ndx file
>by make_ndx. The only reason I can see for this error to come up is if you've
>removed it from the pull.ndx file. If you're using my .mdp file, then
>Non-Protein is a temperature coupling group.
>-Justin
I know there is literature relevant but is there any that explains how to do it in Gromacs?
Look into Justin's Umbrella Sampling tutorial. In step 5 it explain a COM
pulling simulation.
I use for this kind most of the time
pull_geometry = position
but then you must define a pulling direction (vector from 'pull_group0' to
pull_group1').
For the 'pull_dim' i would set all 3 parameters to yes, if you want to do an
afm-pulling experiment simulation. If you're pulling in the z-direction and
have 'pull_dim = N N Y' your pull_group is free to move in the xy-plane (with
no force acting on it), but if you think of an afm-experiment, there would also
be a force-component in the x- and y-direction.
Greetings
Thomas
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