Hi everyone! I want to know whether in gromacs there is a way to pull the ligand up to certain distance from the binding pocket e.g up to 1 nm pulling in z-axis or when the ligand start contacting with the solvent after being pulled? The simulation should stop automatically when the ligand reaches to that particular distance (when being pulled) Is there any parameter which could be defined in gromacs mdp file?
Thanks in advance!
Hi,
there is no parameter to do that. But is easy to set up such an experiment, because knowing the pull rate you basically know how much your ligand is going to move from its original position at a given time. So just limit your MD simulation according to that!
Hello
You should keep in mind that many parameters are implied by the force field. I'd suggest using the same set as in the force field original paper.
Other (such as temperature, pressure, electric fields) you can modify accordingly with the purpose of your simulation.
This link can also help you
https://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html
Dear Md Simulation
As Ricardo J Ferreira said, you can't really stop it once you start pulling. You should pull the ligand along the direction you want, and then if you want to study a particular configuration you can extract the distance as a function of time and take the corresponding frame of the trajectory.
In this way will have a starting configuration with the condition that you want (given distance) and from there you can start a new simulation, be it a free run or a run where you restrain the COM of the ligand at that distance so that you can better study the interaction as a function of the distance itself.
Maybe another approach could be to use the flat-bottom option in the mdp file. It is defined as
At distances above pull-coord1-init a harmonic potential is applied, otherwise no potential is applied.
(see https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#com-pulling). I think you could set
pull-coord1-init = distance_you_want
so that at distances larger than the one you want the ligand is pulled toward the position you want (that is, the given distance set by you), and once it is there then is should remain there, supposing that the force applied by the harmonic restraint is larger enough. In this case I think you should also set
pull-coord1-start = no
so that the distance you set is the exact value and it is not modified by wherever the ligand is at the start of your simulation. Not really sure about this approach, never tried, but maybe it will work.
Hope this helps
Nicola
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