Sayantan Mondal

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Questions related from Sayantan Mondal

How to simulate Stockmayer fluid in GROMACS?

I have been studying the dynamics of Stockmayer fluid under various environment. I used LAMMPS for a project. However, I am wandering if there is a way to perform the simulations in Gromacs. Some...

07 July 2019 9,042 0 View

Why LJ-93 potential form for enclosing wall is different in LAMMPS?

I am trying to create a spherical cavity with soft-sphere potential in LAMMPS. However it seems that this cannot be done. There are other options like lj9-3, lj12-6, harmonic etc. The lj9-3 form...

06 June 2018 1,998 0 View

Is it possible to get very high/low average pressure from NVT simulation of biopolymers?

Hello everyone, I am simulating a protein-water system in NVT ensemble using GROMACS. Prior to that I have energy minimised the system using steepest descent and conjugate gradient methods. After...

01 January 2017 703 5 View

Difference between Total Energy and Conserved energy in GROMACS?

g_energy (or gmx energy) allows us to calculate a lot of system properties. On that list one could find conserved energy and total energy along with other options (like pressure, temperature,...

01 January 2017 880 0 View

Equilibrium Vs. non-Equilibrium MD simulation?

What are the differences between EMD and NEMD? How one decides that which one should be used for a run? I went through some materials available on web but didn't develop a clear concept about...

10 October 2016 2,789 5 View

How to calculate dynamic structure factor in GROMACS?

Is there any way to get dynamic structure factor from GROMACS ? The static structure factor S(k) can be calculated by taking a Fourier Transform of radial distribution function g(r), but I...

08 August 2016 4,077 5 View

Is it possible to simulate protein tagged with a dummy point charge (spherical) or point dipole in water ?

I want to tag a protein molecule with a dummy hard sphere containing some charge or a point dipole instead of that sphere. I don't know if it can be done in GROMACS / NAMD packages. Is there any...

08 August 2016 7,782 1 View

Is there any way to read MD trajectories from a .xtc file (generated using GROMACS) in a FORTRAN code?

I am trying to read trajectories to calculate some properties from a .gro file generated after "trjconv" on a .xtc file in GROMACS. This will be required in a FORTRAN90 code. But the .gro file...

07 July 2016 1,543 12 View

Is there any way to extract electrical dipole moments of individual solvent molecule in GROMACS ?

I need the trajectory of individual dipole moment of ~104 water molecules to calculate single particle dipole-dipole auto correlation function. "g_dipoles" can give dipoles of the total system or...

07 July 2016 8,633 6 View