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 simulation of DNA. Thanks.
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...
05 June 2019 7,291 4 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...
04 May 2019 5,965 5 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...
04 May 2019 2,169 3 View
Can anyone please suggest me review articles/papers/books/links on understanding protein-lipid interactions through Molecular Dynamics simulation ? Thanks
01 February 2018 4,797 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...
01 February 2018 9,699 4 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
31 December 2017 2,318 4 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 ?
31 December 2017 7,382 7 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 !!
31 December 2017 5,947 2 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...
31 December 2017 457 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 ?
11 December 2017 2,664 3 View
How to calculate the RMSD values for a MD simulation using MOE?
07 August 2021 0 0 View
When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.
16 June 2021 0 0 View
Hi. Please tell me what guidelines should i need to follow for questionaries' type research work in India. It is not hospital based work, we are conduction basic institutional based qualitative...
03 March 2021 2,037 3 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
03 March 2021 9,989 2 View
Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...
03 March 2021 5,978 5 View
Hello all, I'm currently working on my undergraduate thesis and I'm having difficulties trying to access KLD Stats and Sustainalytics because my campus Airlangga University and apparently other...
02 March 2021 8,525 1 View