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Questions related to Molecular Dynamics
Hi everyone I try to perform equilibration on my system in AMBER16. I use pmemd.cuda and follow AMBER tutorials. This step is interrupted during execution and remains incomplete. also I have the...
09 July 2021 5,783 0 View
Please let me know some free tools for performing MD for the windows platform. I neither have the expertise in Linux operating system nor I can afford paid tool(s).
05 July 2021 1,741 3 View
Hi guys, iam screening around 1000 compounds in batches using Pyrx. I wanted to know is it possible to in pyrx to load your original grid configuration without manual moving the grid box. Im...
28 June 2021 1,237 1 View
I performed a minimization simulation of a water box using the tip3p water model in NAMD. The water box was in a sphere of radius 20nm and sphericalBCk1 of 10. The water box changed its shape from...
24 June 2021 9,968 2 View
I am trying to explain the allosteric pathway using molecular dynamics. I have tried to do a contact, correlation and hydrogen bond analysis to determine that path (using holo and apo forms). Is...
22 June 2021 3,986 13 View
I want to study the effect of the length of the polymer chain of PMMA on the complex modulus of the PMMA.
21 June 2021 9,108 1 View
I want to analyse the bonding interaction using Lobster COHP analysis. I am done with the calculations. I am trying to follow the LOBSTER manual and it says to use wxDragon to analyse the results....
21 June 2021 7,038 4 View
Hi, Can anyone suggest the optimum level of magnesium ion intracellular concentration in E.coli? Thanks!
21 June 2021 576 0 View
Because, I need the parameters of the Buckingham potential between two similar or different atoms in the simulations of phosphate-based glasses by molecular dynamics, for example, between...
18 June 2021 3,390 7 View
I had a cell that I made a supercell 3,3,3 of it. I did an MD calculation in Lammps, and now I want to see the changes just in the cell that is in 2,2,2 in the matrix of the supercell. How can I...
15 June 2021 8,465 1 View
That is to say the method of synthesis of phosphate-based glass-ceramics doped with Rare Earth Ions.
11 June 2021 3,459 4 View
Dear all. Someone has ever made a calculation of Born Oppenheimer molecular dynamics under the effect of an electric field along a direction.
10 June 2021 8,254 5 View
Dear all, I m looking for a collaborator for performing molecular dynamics of an enzyme and a substrate. Please reply. Thanks Regards, Dinesh S L
07 June 2021 9,211 2 View
What I know is just molar volume and oxygen packing density
05 June 2021 3,003 0 View
Dear colleagues, I have some experience with MD for studies of drug-target interactions, mainly NAMD and Amber. For quite some time, I wanted to try studying the binding/unbinding process of the...
04 June 2021 8,625 3 View
I simulated phosphate-based glasses containing rare-earth ions by molecular dynamics, but when the concentration of rare-earth ions in the phosphate matrix exceeds 8%, the simulation of this...
03 June 2021 1,964 1 View
I need a way to rotate my entire system (DNA and solvent) such that the axis of the DNA lies along the x-axis, but I want the periodic boundaries to be preserved. I added pictures of my system...
01 June 2021 7,343 3 View
I am beginner using Material studio for Performing Molecular dynamics, I am getting stuck in modeling of MWCNT exactly at the centre of an amorphous cell. I am attaching an image below for...
31 May 2021 1,784 3 View
Hello, so far i've come across lots of papers using conventional MD to study stability of protein-ligand binding after molecular docking. What i am curious is, could accelerated MD be used for...
28 May 2021 7,766 3 View
Is there any change that needs to be made to the mdp available in the g_mmpbsa tutorial to calculate the free energy binding of a coarse-grained system (my system is a discoidal lipoprotein) or...
23 May 2021 3,692 0 View
Interaction of residues during molecular dynamics
22 May 2021 9,766 3 View
Hi I have been trying to optimize well-tempered metadynamics simulation in Gromacs 2020.4 engine using plumed, on a transporter from Major Facilitator Superfamily. I have the existing structure...
22 May 2021 3,766 2 View
Hi everyone! The said fatal error stopped my run altogether. It did, however, started minimization. Any idea how to solve this? Thank you so much!
20 May 2021 4,634 1 View
Hi everyone! I'm doing an MD run on Gromacs on HPC and the error attached below popped up. The original rlist was 1.2, and I tried decreasing it to 1, then 0.5, then 0.1, but the same error still...
19 May 2021 3,042 3 View