Sasthi Mandal

6 Questions 13 Answers 0 Followers

Questions related from Sasthi Mandal

Why the membrane is dissociated while doing NVT in gromacs?

Hi Everyone, I got a serious problem while doing nvt run of a plasma membrane in water. NVT run shows the following error: Fatal error: 3 particles communicated to PME rank 1 are more than 2/3...

14 June 2023 7,989 2 View

How to make a dynamic index file in gromacs?

Dear users, I have a system of protein in solution and I want to make an index file of water molecules present within 5 A of the protein. As simulations go on, the water number as well as the...

09 July 2021 802 5 View

Question on natural bond orbital (NBO) analysis?

Hi, I am doing NBO calculation for nanoparticle phosphate interaction. In phosphate group one of the oxygen forms double bond with phosphorus. For this P=O bond, I got three bonding orbitals (BD -...

12 January 2020 6,694 0 View

MD simulation of ZnO

I have seen many literature on MD simulation of ZnO that they have used only lennard-jones or Buckingham potential but not taken any bonded interaction. Could you please explain how the bonded...

01 January 1970 7,185 2 View

Which raman peaks are considered into account from a gaussian calculation?

Hello all, I calculated raman frequency of an organic molecule using gaussian program. There comes a lot of frequency and I am confused that if I have to consider all frequencies or I can exclude...

01 January 1970 2,960 0 View

What is the reason of increasing band gap due to adsorption?

I have a system of biomolecule adsorption on nanoparticle. The HOMO-LUMO gap of nanoparticle increases after adsorption of biomolecule. Here, the charge transfer occurs from zno to biomolecule....

01 January 1970 9,996 0 View