Himanshu Joshi

9 Questions 11 Answers 0 Followers

Questions related from Himanshu Joshi

Any suggestion for the smoother running of VMD?

I am using VMD LINUX_64 OpenGL, CUDA version in my UBUNTU 12.04 64- bit machine. When I load even small structures, say 50K atoms, it becomes slow. The visualization also run with jerks. Earlier...

01 January 1970 255 5 View

Problem with xLeap : Segmentation fault (core dumped)

I am trying to remove some residues from a structure in xLeap with the following command: remove p p.1 where p is the name of unit, But after doing this, as I click to the graphical window of...

01 January 1970 6,291 0 View

Does anyone have experience with calculating the distance between group of atoms using Ptraj in Amber?

I am trying to calculate distance between Center of mass of two groups of atoms located at two ends of my system using distance command in ptraj for AMBER trajectories. For calculating the...

01 January 1970 9,180 2 View

Why only 10 NN free energy parameter?

I didn't understand how only 10 pair were chosen in the 1997 PNAS paper (A unified view of polymer, dumbbell) by Santalucia. I don't know on what basis these 10 sets have been chosen. The...

01 January 1970 7,145 2 View

In order to find the persistence length of a DNA bundle by the formula L=EI/kT, about which axis should I calculate the area moment of Inertia (I) ?

The persistence length L = EI/kT where E = young modulus I = Area moment of inertia k = Boltzmann constant T = absolute temperature

01 January 1970 4,762 0 View

While generating the initail topology and coordinate, when it is better to add ions to the DNA, before or after the solvation ?

While generating the initial coordinate and topology files for DNA simulation in water, we add counter ions to neutralize the backbone charge. I use leap (AMBERTOOLS) to solvate and add ions. But...

01 January 1970 4,407 1 View

Can someone advise on hydrogen bond calculation in VMD for AMBER DNA Simulation?

I want to do some H bonds analysis for my AMBER DNA simulation. I am not sure about its terminology, as it shows only two H bonds between guanine and cytosine in the detail log file which should...

01 January 1970 9,998 5 View

Can anybody describe briefly how to set up a starting structure of PNA for AMBER molecular dynamics simulation?

I want to study PNA using molecular dynamics simulation, can anybody describe briefly how to set up a starting structure of PNA for AMBER molecular dynamics simulation. If any published protocol...

01 January 1970 4,008 1 View

How might one define molarity convention for DNA ion MD simulation in explicit water?

Dear Researchers, I have a doubt regarding the molarity convention used for MD simulation of DNA. I neutralized the charge of DNA molecule with Na+ ions in a water box. I want to simulate the...

01 January 1970 3,519 4 View