How much time required for nvt and npt equilibration in protein ligand compleax MD simulation?

10 October 2018 0 1K Report

I am running a protein ligand complex MD simulation for 10ns. My question is how much nvt and npt simulation time is required before running production run?I am new to MD and gromacs, Any suggestion will be more than welcome.

Badges
Science topic

More Sadaf Rani's questions See All

How to solve restraint failure problem in gromacs?

Dear Gromacs users I am doing a test calculation in MD simulation between ligand and a protein residue for bond angle and dihedral restraints. I have set them in my topology file as below:- ;...

01 February 2020 663 3 View

How to cap a single residue in gromacs?

Dear Gromacs users I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand when I run pdb2gmx it gives me error:- Fatal error: In the chosen force field there is no residue type...

01 February 2020 4,663 3 View

How to solve A list of missing interactions error during free energy calculation using gromacs?

31 December 2019 5,054 4 View

Why editconf removes ligand during box formation in gromacs?

Hi Gromacs users I am trying to set a protein-ligand system in gromacs for MD simulation. I took topology and gro file from an external source. Now I combine the gro file of ligand and protein...

10 November 2019 6,078 8 View

How can I get protonation states of protein and ligand using pdb2pqr webserver with propka 3.1?

Dear researchers Need your expert suggestions please. I am trying to get protonation states of my protein ligand by using pdb2pqr webserver version 2.1.1. However; when I get result propka file...

07 August 2019 4,817 12 View

How to set input for minimisation in amber having protein frozen?

I want to run MD simulation of my protein that is 479 a.a long. I found 6 bad contacts in my protein by the process mentioned in tutorial....

04 May 2019 7,724 10 View

From where to find scp -r ~yuchzhou/AMS536/AMBER_Tutorial/002.ANTE.TLEAP/rizzo_amber7.ionparms ./ ?

I am following amber tutorial with HIV protease Can any one suggest me from where I can find this particular file?mentioned in this command Copy parameters of ions to your working directory...

03 April 2019 3,919 4 View

How to install Network 1.11.x version for python?

I am trying ligand protein gromacs tutorial for my protein ligand MD when I come to the command python cgenff_charmm2gmx.py JZ4 jz4_fix.mol2 jz4.str charmm36-nov2018.ff it says that This script...

03 April 2019 4,523 1 View

How to combine tpr files in MD after restart?

I started protein ligand MD simulation in gromacs for 10ns. However due to cluster shutdown I had to restart it again. Md.tpr file of md is formed but it do not include portion after restart; How...

01 February 2019 9,527 3 View

Why nvt equilibration starts from step zero after a restart?

I am running a protein ligand MD simulation using gromacs. I have started npt equilibration for 500000 nsteps (1ns). After a computer shutdown at 170500, I started restart using following...

09 October 2018 1,107 1 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View