Strange Surface in NCIPLOT/VMD. Any idea?

More Ranajit Saha's questions See All

Is this 6GHz wifi antenna create complexity at the time of febrication?

I have design a 6GHz antenna for wifi.The feed line width is 2mm and there are 2 parasitic elements beside this feed line with 1 mm gap.Is there any problem at the time of febrication?

04 February 2021 9,241 3 View

How can you make a PEDOT:PSS film using the doctor blade technique?

I have been trying to make an even PEDOT: PSS (PH1000) film with the doctor blade technique (tape casting) with varying results. I have been using a silicon substrate that's treated with piranha...

01 February 2021 8,506 5 View

How robust are open source soil moisture sensors connected to an arduino board for field monitoring?

Seeking recent experiences in the development and deployment of low-cost soil moisture sensors (ideally under $50/sensor) connected to arduino-based dataloggers. What is the longetivity of the...

19 January 2021 6,256 2 View

How to separate a mixture of organic acids by GC?

I would like to develop a method for analysis of many organic acids in the same time. how to separate the chromatographic peaks of each one?

20 December 2020 8,399 3 View

Should I keep the missing values > 50%?

I have a data set of 771 sample size. But some of the variables (laboratory findings like ALT, AST, creatinie level) have more than 50% missing values. Should I drop those? But I think those...

13 December 2020 4,847 3 View

How to Strip off HSQ( Fox 16) after etching?

We are finding a hard time to strip of residual HSQ ( Fox 16) after using it as a mask in etching? We are coating 600 nm thick HSQ and writing with 3000 microC/cm^2 dose at 1 nA current. We are...

08 December 2020 5,452 2 View

Why the oral cancer cell line from metastatic tongue origin is showing less aggressive property?

I am working with oral cancer cell line SCC090 (ATCC). As per ATCC data sheet it is originated from metastatic tongue. It's primary site is not mentioned. Due to the origination from metastatic...

08 December 2020 5,674 3 View

In case of larger sample size (more than 700 sample) can I do t-test though the data is not normally distributed?

My sample size is more than 750 but sk test is showing non-normal distribution. The variables have several outliers but I shouldn't remove those. In that case what should I do? t-test or other...

06 December 2020 1,285 19 View

Why the western blot of HIF1alpha of the whole cell lysate shows intense band under normoxia without any induction of hypoxia?

I am working with oral cancer cell lines and trying to find the expressional changes of HIF1alpha under different experimental treatment. I am getting intense band of HIF1alpha in the western blot...

29 November 2020 5,707 3 View

How to calculate in-plane lattice strain for 2D material?

I am working with h-BN and need to find out the strain due to in-plane lattice constant. The famous Williamson-Hall method may not be applicable here as it analyzes XRD for calculation of strain...

19 October 2020 7,386 4 View

How to find out the problem of VMD software when i run it?

Hello I try to install and run the VMD software on windows 10 (64-bit).It doesn`t work and it is closed when I run it. I checked all of tutorials, videos and documents. But they did not work...

22 February 2021 8,211 3 View

Rdf of atoms from a COM or point in lammps or VMD?

Hello all, as I understand there isn't any straight way to get an rdf of atoms from the center of mass or a coordinate of specific atoms in lammps. I wonder if anyone know any trick or way to get...

16 February 2021 2,517 2 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

31 January 2021 6,321 1 View

How to script VMD tcl within bash script?

Greetings, I want to run a vmd script within my bash script. I am using the text only version of VMD for linux for my windows terminal ubuntu subsystem and I would like to generate code within my...

16 January 2021 192 5 View

Recognition of Molecules from a file containing molecular dynamics trajectory?

Can anyone recommend a good code/software/implementation to identify the change of molecules (bond creation/break, number of molecules at a given timestep, etc.)? I am currently working with XYZ...

12 January 2021 1,655 4 View

How to increase GPU usage during MD simulation?

The GPU usage percentage of my Nvidia Quadro K3100M does not exceed 10% during running MD simulation of protein of 252 residue length using VMD/NAMD software. Any one can provide advice on how...

08 January 2021 7,594 3 View

How to minimize the standard deviation of protein-ligand complex using mmpbsa (CaFe 2.0 vmd plugin) using namd?

Hello, I wanted to know how can I minimize the standard deviation (SD) of my simulated protein-ligand complex of 50ns using MM/PBSA method of Cafe 2.0 plugin of VMD plugin using NAMD. I have tried...

10 December 2020 8,132 1 View

How to prepare a solvated Nano-porous graphene sheet system for LAMMPS using VMD?

Hi, I am going to perform MD simulation for the Nanoporous Graphen sheet. I know how to make the pores in VMD. But when I tried to make the data file it was lacking a lot of parameters such as...

20 November 2020 3,629 2 View

How converted .inp charmm file to .top Gromacs file ?

I want to simulation cytochrome C that it has two parts HEME and protein. I have charmm files par_heme.pdf and top_heme.pdf heme group but I do not know how to convert pdf file to *. inp because...

13 November 2020 7,955 2 View

How to change the protein chain names X into A, B, C, D after MD simulations in Gromacs?

I am running MD simulations for holoenzyme in Gromacs. The protein has four chains like A, B, C, D. After MD simulations, All the chains are showing as X chain in VMD and even in the PDB file....

12 November 2020 6,228 1 View

Tian Lu

Perhaps this is a program bug. Latest version of Multiwfn (http://sobereva.com/multiwfn) fully supports NCI analysis for periodic system, if you upload your .xyz file and show me translation vectors of the cell, may be I am able to show you how to correctly plot NCI map via Multiwfn+VMD for your system.

PS: Recently I have a blog article to describe how to perform NCI and IGM analysis for periodic systems: http://sobereva.com/588 (in Chinese)

Riaz A. Khan

Seems some of the atoms were not recognized during the generation of the plot. It may also be a bug as Tian says.

Hilal Kucuk

I know it is any related question. Sorry for it, I wonder can we calculate the non-covalent interactions (NCI), more precisely the amount of hydrogen bonding, van-der waals interactions and steric repulsions? I know I can plot it but can we see their amount in output?