Md Simulation

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Questions related from Md Simulation

Steered MD pulling in Gromacs ?

Dear all I have few confusions about the pulling code in gromacs, I was using NAMD before and the method was quite straighforward in NAMD to pull the ligand out of the protein, in gromacs it is...

07 December 2021 495 1 View

Kinetic off rate koff from Bell Evan Equation ?

Hi I have attached the link to article and the table from the article with this question, I wanted to know how the value of 0.7 s-1 is calculated from the slope and intercept values using the bell...

02 December 2021 9,024 1 View

Stop the gromacs pulling simulation when the ligand being pulled reaches to certain distance?

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...

20 October 2021 5,542 3 View

What is the best way to replicate the trajectories with new velocities in gromacs?

What is the best way of repeating simulations, say I have to run the 10 replicates of the same simulation trajectory which was previously simulated for 100 ns production run after minimization and...

30 August 2021 9,331 3 View

How to get the rupture force vs loading rate plots through SMD simulations from gromacs?

Hi I have force vs time graph and Pulling com positions vs time graphs and got from SMD simulations in gromacs the pulling velocity I am using is constant at 0.01 and the force constant was 1000...

17 January 2021 9,335 5 View