S. Xavier

46 Questions 51 Answers 0 Followers

Questions related from S. Xavier

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?

09 September 2019 5,074 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...

06 June 2019 8,633 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?

01 January 2019 1,483 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?

12 December 2018 6,233 7 View

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

11 November 2018 804 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?

02 February 2018 9,454 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)?

11 November 2017 4,943 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...

10 October 2017 3,384 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?

10 October 2017 2,495 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...

09 September 2017 9,469 3 View

How to run MD simulations using gromacs in SUN GRID ENGINE (SGE)?

How to prepare the script file, namely job.sh while submitting it as qsub job.sh to SGE using single processor? How to set GROMACS environment in the script file?

08 August 2017 5,067 1 View

MD simulations through web?

How to do protein ligand simulations through web?

05 May 2017 10,069 2 View

Clarification in pull code of umbrella sampling?

When the pull_coord1_dim = N Y Y, should the pull_ncoords be equal to 2?

03 March 2017 6,153 11 View

How to install G_MMPBSA in Windows 7, 64 bit ?

What are the steps to install ABPS and MMPBSA in Windows 7, 64 bit using cgywin?

03 March 2017 6,313 2 View

What are the steps for linear interaction energy to calculate gibbs free energy in protein ligand system in gromacs?

Linear interaction energy =================== How to define energy groups in protein ligand complex (solvated in water) and ligand in water?

03 March 2017 8,146 5 View

Can anyone suggest books/papers regarding Radial distribution functions of solid, liquid and gas?

How to interpret the graph of Radial distribution function?Using gromacs, had obtained the RDF of my organic compound of interest. How to analyze the graph?

02 February 2017 1,585 2 View

What are the steps for umbrella sampling of protein ligand complex in simulation dynamics?

Steps for umbrella sampling of a protein ligand complex

02 February 2017 2,192 3 View

How to prepare residue topology file for any organic molecule, as the first step in gromacs?

How to prepare the input file in gromacs?

01 January 2017 7,573 5 View

How to convert .top file and .crd file to gromacs input file using acpype?

$ /usr/local/acpype/acpype.py -p com_solvated.top -x com_solvated.crd -b complex -d=================================================================================================| ACPYPE:...

01 January 2017 5,435 0 View

How to run gromacs in windows using cygwin?

Had installed gromacs in windows..How to run a test code using cygwin command prompt? Can some one help?

01 January 2017 6,136 4 View

Does inductive effect influence the vibrational modes in an organic molecule?

How hyperconjugation affects the vibrational modes in an organic compound?

11 November 2016 2,595 1 View

How to install PACKMOL in Windows 7, 64 bit computer?

PACKMOL software

10 October 2016 1,327 2 View

How to use fix npt command in LAMMPS?

In order to calculate Mean Square displacement, for an organic molecule containing 29 atoms, how to define fix npt and fix langevin?

09 September 2016 665 4 View

LAMMPS WARNING: Bond/angle/dihedral extent > half of periodic box length. How to rectify it?

simulations

09 September 2016 7,617 3 View

How to define bond co-efficients when bond_style is morse? How to obtain the values of bond coeffs for C-N, C-C, C-H and C-O bonds?

simulation dynamics, LAAMPS

09 September 2016 457 8 View

How to generate electron density difference map (EDDM) using gaussian and gausssum?

ELECTRON DENSITY DIFFERENCE MAP

09 September 2016 8,427 0 View

How to obtain MSD accurately in lammps?

Should it be a straight line?

08 August 2016 4,728 6 View

When bond_style harmonic is used in LAMMPS, E = K (R-r0)^2 is the formula. How to calculate K (in Kcal/molnm^2)for O-H, N-H, C-N, C-O?

LAMMPS

08 August 2016 8,650 0 View

How to calculate LJ potential parameters for C-N bond, C-C bond, C-H and N-H bonds ?

For pair_coeffs in LAAMPS (molecular simulation dynamics)

08 August 2016 5,643 2 View

Should we explicitly define volume, temperature and pressure in LAAMPS, for calculating enthalpy of a system of identical molecules. How to proceed?

Molecular simulation dynamics

08 August 2016 8,220 4 View

What are the books which explain the vibrations of cyclic amines?

Cyclic amines

07 July 2016 2,637 0 View

How to compute PES scan for two different dihedrals simultanously using Gaussian to obtain a 3D plot?

Potential energy surface scan , Gaussian software

07 July 2016 896 1 View

UV in solid phase gives a single peak. Whereas, UV in ethanol solution gives two peaks (there is a splitting). Does ethanol react with the sample?

07 July 2016 3,919 3 View

How to use an entirely different basis set in gaussian (B3LYP/SNSD)?

BASIS SET

06 June 2016 977 1 View

How to convert pdb file to lammps input file using VMD software?

molecular simulation

05 May 2016 7,544 0 View

During potential energy surface scan, we get negative energy values. What do they imply?

05 May 2016 5,628 2 View

Why the unscaled wavenumbers are very high?

Gaussian

05 May 2016 5,701 0 View

How can we calculate the protein-ligand thermodynamics in molecular docking?

protein-ligand thermodynamics

05 May 2016 9,944 3 View

How to use OVITO software for molecular simulation dynamics?

molecular simulation dynamics

04 April 2016 5,155 2 View

In case of C1 group symmetry, how do we assign the vibrational modes? Do we use only A' for all the modes?

Group symmetry

03 March 2016 9,092 2 View

Is the Zero point energy and energy of optimization are one and same?

The optimization is done in the Gaussian software and we calculate the energy. Can the energy of optimized structure be considered as zero point energy of the molecule?

02 February 2016 7,049 7 View

What is the sharp link stays between spectrocopic techniques and quantum computational methods?

Is there any link between spectroscopic techniques and computational data obtained from approximation methods.

01 January 2016 5,266 0 View

The calculation in gaussian is unending when VCD is ticked. Is there any other method to plot VCD when the molecule has chirality?

chiral carbon

08 August 2015 9,203 0 View

Can a molecule be considered be as single entity?

Because every molecule in nature is somehow or other connected or attracted or in affinity with other system of molecule. In computational chemistry we consider and analyse molecule as single...

04 April 2015 9,198 4 View

Can anyone tell me what is the best basis set to run polycarbonate samples?

I am working on the polycarbonate compound. I would like to know which basis set will give me good data closer experimental values of frequency, geometrical parameters, reactivity details and...

01 January 2015 791 4 View

What are the differences between the electronic and the optical properties in a UV-vis study?

Homo-LUMO study.

05 May 2014 310 3 View