Nandan Kumar

8 Questions 39 Answers 0 Followers

Questions related from Nandan Kumar

Missing pulling information while performing Steered Molecular Dynamics ?

Dear all, This is regarding the Steered Molecular Dynamics. After finishing SMD, extracted useful frames from the SMD trajectory and performed the brief NPT equilibration of the selected useful...

12 December 2019 6,830 2 View

Is there any other way to calculate the surface area per lipid of 200 ns trajectory, other than using MEMPLUGIN of VMD?

Hi Everyone, I am calculating the surface area per lipid of 200 ns membrane trajectory using MEMPLUGIN of VMD and it seems to be calculating the same too slow. Therefore, I would like to ask Is...

06 June 2019 3,430 4 View

CCSD(T) calculation of Open shell singlet cation ?

I would like to calculate the energetics for open shell singlet Sc+ and Sc+(OH2) using CCSD(T) level. As if we consider default Gaussian procedure, it seems to be considered close shell singlet....

12 December 2018 8,962 0 View

Calculate Radial Distribution Function using ONIOM gaussian results

Dear all, I would like to ask to you all that I am performing the ONIOM calculation and want to calculate radial distribution function. So, Please let me, can I calculate radial distribution...

07 July 2017 1,294 0 View

How can one continue the MD simulation in Gromacs if simulation has terminated, but not completed?

I am running the MD simulations for 30 ns which is 15000000 nsteps using dt= 0.02 using GROMACS software but it has terminated (after 13000000 steps) before completion due to queue limits. I would...

06 June 2017 7,434 10 View

Can anyone suggest me what type of atoms of phospholipid headgroup have to select for lipid headgroups density analysis?

As we know that density analysis is one of the worthwhile analysis to validate the our bilayer membrane model. I am using the gmx density of gromacs software to calculate the lipids headgroup...

06 June 2017 2,015 1 View

How can I get torsion potential?

Basically, I want to calculate the torsion angle potential (Vn) for the force field parameter development. For that I performed the potential energy surface (PES) scan with rotating a bond by 360...

12 December 2016 6,551 13 View

How do we calculate -center x y z (Coordinates of geometrical center), when we orient the protein in bilayer membrane?

I need to construct a mixed lipid bilayer for simulating a membrane protein. I am trying in GROMACS, but I have a problem in orientation of protein in lipid mixed type lipid bilayer.

06 June 2015 3,682 4 View