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Questions related from Roshan Shrestha
Hi all, I am working on a MD simulation of a membrane protein inside the POPC bilayer using namd. At first, I ran a short constrained dynamics by applying harmonic constraints to both...
06 June 2019 7,392 4 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...
05 May 2019 2,403 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...
05 May 2019 6,062 5 View
Can anyone please suggest me review articles/papers/books/links on understanding protein-lipid interactions through Molecular Dynamics simulation ? Thanks
02 February 2018 4,898 3 View
Is there any standard value like two non-bonded residues or atoms are considered to form a contact if their distance is less than ? I usually use like 1.4 nm for short range non-bonded LJ cut-off...
02 February 2018 9,811 4 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 !!
01 January 2018 6,048 2 View
I want to rotate a specific residue (say "resid 7 and resname MET") by 180 degrees around x-axis and save the coordinates. Can it be done using VMD's TK Console ?
01 January 2018 7,546 7 View
I want to measure the tilt of helix with the normal of bilayer. My system is basically a dimer with two helices. Since using sidechain atom relative to the axis is optional, I simply defined...
01 January 2018 680 3 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
01 January 2018 2,483 4 View
After running my previous simulation yet again after making some minor changes during NPT equilibration, I've attached here with my plots for RMSD. The RMSD plots look promising, but still can't...
12 December 2017 1,951 4 View
I used contact map plugin in VMD to generate a contact map, but is there any modification we can do to get publication quality image of the map like changing colors etc. It simply gives me a...
12 December 2017 8,276 4 View
VMD's contact map plugin allows me to save the data in postscript format, but is there anyway I can write out the data straight from VMD's Tk console or something so that I can plot the data...
12 December 2017 8,625 0 View
I used gmx trjconv -b 100000 -e 150000 -f wild_nopbc.trr -s NPT_wild_0_eq.tpr -pbc mol -o wild_100ns_150ns.trr to get equilibrated trajectory over 50 ns from 100 ns to 150 ns. Is there any way to...
12 December 2017 5,013 2 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...
12 December 2017 8,931 3 View
I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Is there any way to get COM...
12 December 2017 6,325 3 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 ?
12 December 2017 2,775 3 View
I've attached here with the RMSD plot for the C-alpha atoms of membrane protein after running a 100 ns production run simulation. But, I don't know what to make of it. I don't think the RMSD is...
11 November 2017 509 8 View
It is my sheer stupidity, but though I've my initial .tpr file for running the simulation and final .gro structure after the simulation, I think I may have lost my initial .gro structure before...
11 November 2017 9,286 2 View
I am trying to understand the difference between these potential energy and free energy landscapes like how these surfaces can be created and what kind of information can be drawn from these two...
11 November 2017 4,045 5 View
I want to obtain contact map in VMD for finding helix-helix interaction in my Dimer simulation. I know that I can use VMD to do this via: Extension->Analysis->Contact Map, but how to select...
11 November 2017 1,305 1 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...
10 October 2017 7,957 5 View
Dear all, Here I have attached with the RMSD for 100 ns production run of membrane protein simulation taking C-alpha atoms for both least square fitting and as a reference structure....
10 October 2017 4,001 5 View
I've performed MD simulation of transmembrane protein using Gromacs. Here, I want to calculate the angle of tilt of the transmembrane protein against the bilayer normal. What are the ways of...
10 October 2017 5,551 3 View
The default unit for RMSD in gromacs is in nanometer (nm). Since I use Xmgrace for plotting my results, is there any way to obtain my RMSD value in Angstrom rather than in default nanometer (nm)...
10 October 2017 9,732 3 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 1,960 5 View
Is there any way to extract the individual information like Pressure, Energy, Temperature etc from log file of molecular dynamics simulation in NAMD so that I can save them in either .dat format...
09 September 2017 9,550 3 View
I want to attach methyl forming covalent bond with Oxygen of Guanine in DNA. How can we do it using Avogadro ? Thanks
09 September 2017 2,328 0 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...
09 September 2017 3,440 13 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...
09 September 2017 2,666 3 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...
09 September 2017 247 5 View
Here, I have attached a conf file for the minimization of my structure in NAMD. From my previous experience of working with Gromacs, it uses the output of the minimization for equilibration and...
09 September 2017 3,396 4 View
I have a simple 5 ns molecular dynamics simulation run of protein ligand complex using NAMD. How can we visualize the hydrogen bond formed between the ligand and the residue (say [ARG120]) in vmd ?
09 September 2017 9,971 3 View
Are there anyone who have experience on installing Matpack, C++ Numerics and Graphics Library ? I want to use this program to plot my data obtained from Gridmat-MD, for lipid bilayer analysis. I...
07 July 2017 8,851 2 View
I am really struggling to give inputs in http://www.charmm-gui.org/?doc=input/membrane_only&step=1 for generating the lipid parameters for POPC compatible with CHARMM 36 force field as in...
10 October 2016 1,739 5 View
I have a 3D structure of Biphenyl from Chemspider. I want to convert it into .mol2 format using openbabel in my Ubuntu linux system. What is the procedure to directly convert it into .mol2 format ?
09 September 2016 4,300 2 View
Most of the papers I have read on MD simulation of DNA is based on CG simulation. I am wondering if all atom atomistic simulation of DNA is viable or not and what are current research topics on MD...
09 September 2016 4,698 0 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...
08 August 2016 3,534 6 View
I used to use either grep command or manually delete "HOH" to remove water molecules from my pdb file. However, I am not sure how to remove water from .gro file. The file is attached here. Thanks
01 January 1970 9,482 3 View
