MD simulations through web?

More S. Xavier's questions See All

What are the steps to calculate bond dissociation enthalpy in gaussian?

For example, in phenol, how to calculate the bond dissociation enthalpy of each bond using gaussian? What are steps?

08 September 2019 4,731 3 View

Why the theoretical values (vibrational and NMR ) obtained through Gaussian is greater than experimental values?

Why the theoretical values (vibrational and NMR ) obtained through Gaussian is higher than experimental values? NMR was computed using GIAO technique and vibrations were calculated using B3LYP...

05 June 2019 8,487 5 View

What are the books/papers to learn about quantum confinement in 1D, 2D and 0D nanostructures?

What are the books/papers to learn about quantum confinement in 1D, 2D and 0D nanostructures? What are books/papers to know more about nanoelectronic devices?

31 December 2018 1,370 8 View

How to proceed with molecular dynamic simulations in nanoscale?

How to commence simulations in nanoscale? In which part of the code do we introduce the nano dimensions?

11 December 2018 6,127 7 View

How to calculate thermal and electrical conductivity of an organic compound using Molecular dynamic simulations?

10 November 2018 671 4 View

How to view the conformational change in the protein after MD simulations of protein ligand complex?

How to view the conformation change in protein after 50 ns MD simulations?

01 February 2018 9,363 3 View

In gaussian calculation, what does negative polarizability of an isolated molecule indicate?

In Non-linear optical activity what does negative polarizability of an isolated molecule indicate (through gaussian calculation)?

10 November 2017 4,793 1 View

How to make a Journal indexed in Scopus?

We have multidisciplinary Journal in the college (St. Joseph's Journal of Humanities and science). We publish Research articles in all the disciplines. Till now we have published 8 issues as four...

09 October 2017 3,274 5 View

What is meant by pi-alkyl, pi-pi T shaped and pi-Sulphur interaction in protein-ligand binding?

Can anyone suggest books/papers which clearly explains pi-alkyl, pi-pi T shaped and pi-Sulphur interaction?

09 October 2017 2,225 4 View

How to fix the following mpirun error?

I do MD simulations in SGE cluster using gromacs 5.0.2 version. After exporting the path and libraries correctly, I gave the following commands gmx grompp -f mdp/eql2.mdp -o eql2 -pp eql2 -po...

08 September 2017 9,335 3 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

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

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Krishnendu Bera

Gromacs:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/

Amber

http://ambermd.org/tutorials/

Namd

http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf

For any more help you can write to me.

S. Xavier

Thank you for your response.