22 Questions 28 Answers 0 Followers
Questions related from Roshan Shrestha
I have an infinite CG model of the material solvated in water. I am trying to apply a uniaxial deformation along a particular x-axis; the mdp settings in gromacs are below. tcoupl...
15 February 2023 5,930 1 View
I have a coarse-grained model of a surface which is almost planar/flat in 2D. Now, I want to compute some of its mechanical properties to test it. Young's modulus is one of the properties that...
09 May 2022 6,340 0 View
Hi, Can someone suggest me the recent/good work(papers) done either experimentally/computationally using MD Simulations for the measurement of bending modulus of graphene? Thank you. With...
08 December 2021 1,344 3 View
Hi everyone, While using the PDB reader of charmm-gui for my membrane protein system which is a dimer, I got stuck at PDB manipulation option. It gives me option regarding...
29 May 2019 9,516 3 View
Hi everyone, My system is a dimer. During the MD simulation, I can see a strong hydrogen bond formed between two lysine residues which are at the side chains of two peptides. But, the issue is...
24 May 2019 7,240 2 View
Can anyone please suggest me review articles/papers/books/links on understanding protein-lipid interactions through Molecular Dynamics simulation ? Thanks
22 February 2018 6,206 3 View
The characteristic frequency of thermal motion is around 7E12 Hz at room temperature (300K), but from that information how can we conclude that the bonds are hard; they don't vibrate !!
22 January 2018 4,816 2 View
Are there any scripts or tools available in python to plot the running average of the data similar to as shown in the figure attached? Thanks
02 January 2018 1,791 5 View
Are there any gromacs or other tools available to look for or find the number of protein-lipid contacts during Molecular Dynamics simulation of membrane protein ?
27 December 2017 2,804 3 View
I have attached here with the .ps file that has heatmap data in it. Is there anyway I can extract the data from the file. I tried with Inkscape, but it is not opening in Inkscape.
20 December 2017 8,381 4 View
I tried to perform a simple energy minimization of nanotube with water molecules in it. The initial psf and pdb files are taken from the NAMD's nanotube tutorial. After I ran the energy...
05 December 2017 4,356 3 View
I've created a membrane protein system which is shown in vmdscene.png, but I want to produce a publication quality image of such system using VMD as shown in image popc.png. I want to increase the...
20 October 2017 7,932 4 View
I want to create a representation in vmd to view only the hydrophobic (non polar) region of lipid bilayer. How can we do that ? Also, can we measure the length of that hydrophobic region using vmd.
12 September 2017 5,767 4 View
I am running a 10 ns NVT production run MD simulation of a protein in NAMD. Everything looked fine till 9 ns, but during the end of the simulation, while running the dcd in VMD, it seems like the...
10 September 2017 2,184 12 View
I am running a typical MD simulation of a protein ligand complex in NAMD using OPLS-AA/M force field and its parameter. I want to study the change in conformation of the receptor during MD...
09 September 2017 6,705 3 View
Here I have attached the screenshot of the simulation where a bond is shown between N-terminus and C-terminus atoms. I want my background to be white, so unfortunately, the default color of the...
08 September 2017 2,014 2 View
Here, I have attached snapshot of my system after running energy minimization in NAMD. The problem that I continually have been facing is to see my system out of PBC box when I use the command pbc...
07 September 2017 5,664 5 View
Hello everyone, I mostly use charmm gui to create psf files for proteins and for building bilayer. This time I wanted to create psf for a ligand using charmm gui, but an unknown problem is shown...
12 August 2017 4,233 3 View
I used gromacs to perform a 10 ns equilibration of POPC membrane. I've heard that we can use gmx density to get the bilayer thickness. I would be very grateful if anyone can suggest me how to use...
22 July 2017 6,234 5 View
I want to use Coarse Grained Molecular Dynamics simulation to study protein membrane simulation. However, is it correct to use coarse-grained structure for lipid bilayer and atomistic structure...
27 August 2016 216 5 View
Hi, I am currently trying to pull a box in X-direction with these settings in my mdp file of gromacs. tcoupl = v-rescale tc-grps = System tau_t...
01 January 1970 2,592 0 View
I have been looking for theta solvents for some of these Nylon polymers in the literature, but except for Nylon - 6, I couldn't find much information. Can anyone working in Polymer...
01 January 1970 6,446 2 View
