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Questions related to Molecular Dynamics
I am doing my Ph.D. in Materials Science and am completely new to Molecular Dynamics Simulation and Linux. I am using Manjaro Linux 20.1 and have Gromacs 2020.4, VMD 1.9.3, packmol 20.0.10,...
29 October 2020 1,794 3 View
Hi all, Consider a circular plate's deformed configuration is available, and we know somehow the undeformed shape (perfectly flat with a defined radius). Is it a way to estimate average forces on...
28 October 2020 4,269 5 View
I have a question. I want to measure the volume per lipid. I built a membrane with water and run the simulation for 300 ns. To measure the volume per lipid I used a .gro file from the simulation...
23 October 2020 2,626 3 View
Hello everyone, I am trying to replicate the process done in the paper 'Shocks near jamming' by Gomez et al (PRL, 2012) where the granules are initially in a pre-stressed state with initial...
22 October 2020 1,410 1 View
I am trying to calculate some hydrodynamic properties from MD results. Part of the process in to calculate the transvers current correlation function which is formulated as C(q,t)=⟨J∗(0)J(t)⟩ ....
13 October 2020 4,833 1 View
I am trying to perform a surface lapping process on LAMMPS molecular dynamics software for my final year undergraduate mechanical engineering project. I am having trouble finding the potentials...
05 October 2020 2,697 2 View
I would like to simulate the formation of polymer nano-complex using two biopolymers and find the effect of the concentration of both the substrates on the particle size of that nano-complex in a...
03 October 2020 10,067 1 View
I am very new to this field and would be grateful if you could help me to give a head start. I have been following this tutorial from Youtube (https://youtu.be/GXA2PyqKYdY?t=405) and whenever I am...
21 September 2020 4,805 4 View
I am simulating the pulling of two nanoparticles in a polymer. I get the attached PMF curve, showing a secondary (and much deeper) potential well. I was wondering if there is a physical...
20 September 2020 7,792 5 View
What is free software for protein-ligand molecular dynamics simulation to publish in a peer-reviewed journal?
15 September 2020 4,869 3 View
I am trying to simulate an adhesion test using LAMMPS on an ice-Aluminium structure and my script runs fine until I introduce a specified region on which I apply a force in the y-direction using...
08 September 2020 5,203 2 View
I tried to download VMD version 1.9 as it wouldn't require things for my computer to process. I did the necessary steps to install it and it finally said "VMD installation complete, Enjoy!"...
07 September 2020 6,893 2 View
I would like to know if it is possible to do MD calculations for protein on a regular PC? If it is possible, then what are some of the software that can be used and if there is anything i need to...
06 September 2020 1,739 6 View
Dear Sir/Madam, I am using Targeted Molecular Dynamics of NAMD for my simulation. It requires me to provide an initial RMSD between two structures ( two states of a protein structure). Can anyone...
28 August 2020 9,360 3 View
Dear all, I am a beginner in Molecular Dynamics. I build a pre-reaction epoxy model using Materials Studio and plan to perform the cross-linking procedure using Lammps. However, the msi2lmp tool...
27 August 2020 7,938 1 View
Hi, I'm trying to attach a carbonyl linker to Lys so that I can attach a PEG molecule to it. I have attempted so far by combining Lys , N-terminal and C-terminal topology data . But I'm having...
25 August 2020 8,546 1 View
I am trying to CG relax a amorphous GeSe system with B3LYP and single K-point (gamma). Even though I have a 250 atom model, the calculations seem to be extremely slow. Is there a way to speed up...
24 August 2020 9,111 4 View
In gromacs gmx order computes the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. then we use this S mol = 1/2(3cos^2 (θ ) − 1),. So to...
02 August 2020 6,195 2 View
the atom order in ligand shows mismatch and thus i cannot proceed to next step
01 August 2020 9,147 6 View
CHARMM GUI online does a protein-protein interaction where you can measure the interaction energy of one chain with all the others. Is there a way to do this for each residue? Basically I want to...
30 July 2020 9,119 3 View
Adsorption run calculation Automatic charge group calculation failed. No charge groups have been calculated. The particles that are being considered for a charge group are not charge...
30 July 2020 9,320 0 View
Hi. I'm new to GROMACS and I want to simulate a DMPC bilayer contains 8 Cholesterol molecules. But I have no idea about how to add Cholesterol molecules to my simulation box.
08 July 2020 5,969 1 View
Hi everyone I'm new in all the field of molecular dynamics, but i trying to run a SMD of one protein with two isopeptide bond, one in each domain, that prevent my protein stretch. My problem is...
08 July 2020 6,666 3 View
I have tried all the things mentioned in the official website and also I installed cygwin (linux emulator) and tried running there. But it was also a failure.
01 July 2020 3,468 2 View