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Questions related to Molecular Dynamics
Trying to simulate a ice-PTFE interaction and am unable to find a reference which actually lists out forcefield parameters for PTFE-PTFE interactions using ReaxFF or even other force fields like...
09 February 2021 9,679 2 View
GROMACS version: 2018.4 GROMACS modification: No I have a question. I want to know one thing. How is computing autocorrelation function, because I am not sure about something. I try to calculate...
08 February 2021 9,787 1 View
Hi, I am about to do energy minimization but the above error occurred, I checked my .mdp file and .top file but could not find the problem. TOP file ; Include forcefield parameters #include...
02 February 2021 1,222 3 View
I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...
01 February 2021 6,614 1 View
I have created an Ice 1h structure and am equilibrating it 100K in NVT ensemble in LAMMPS for a timestep of 0.25fs in 3000 steps. The potential used is TIP4P/Ice. Although the simulation runs fine...
27 January 2021 9,852 11 View
Hi all, Is there any software or webserver to read the molecular dynamics (MD) simulation trajectory which obtained from Ab initio MD simulation to calculate the atom-atom radial distribution...
26 January 2021 9,861 3 View
I am a beginner in the field of molecular dynamics and biochemistry. I need the parameters such as van der Waal radii, partial charge of each amino acid. How do I read directly the parameters from...
21 January 2021 3,804 3 View
I try to simulate FTIR spectra for polyethylene from molecular dynamics (namely LAMMPS) by Fourier transform of dipole moment.I have gained FTIR for nonreactive force fields,but reactive...
20 January 2021 4,941 2 View
Selfconsistent noncollinear magnetic calculations can be done in VASP. I am wondering how VASP update the spin directions at each local site. For molecular dynamics, VASP search the next...
17 January 2021 1,743 3 View
I'm trying to study the effects of desiccation on some proteins, could someone tell what solvent or what simulation conditions I should set up to simulate a desiccation environment on GROMACS.
06 January 2021 7,335 3 View
I need to calculate the radial distribution function for my system which includes 50 molecules. Here is my code line to generate rdf in gromacs: gmx rdf -n Index.ndx -f mdrun1.xtc -s mdrun1.tpr...
05 January 2021 5,198 8 View
I am working with molecular dynamics in a nanotube but I need easy to use software to be able to homo lumo, molecular dynamics and also charge densities in a chemical doping, I am also looking in...
31 December 2020 7,724 1 View
Which one is the best and most user friendly tool for Molecular dynamics?
25 December 2020 3,019 7 View
I have a box let's say full of toluene, I want to measure the angle between toluene molecules versus distance. I think I should use "gmx gangle"; however I am a bit confused about how to select my...
21 December 2020 8,645 4 View
I've generated a set of maps for my receptor using ADT (AutoDockTools). It has resulted in the files: .A.map .C.map .HD.map .N.map .NA.map .OA.map .SA.map .d.map .e.map But when I try loading the...
21 December 2020 8,099 2 View
Hi there, I'm looking for interatomic potentials for the stimulation of metal oxide bonds, I have already used Pedone potentials and Teter potentials, I was hoping to use another one but I can't...
06 December 2020 8,498 2 View
I'm looking to get specific energy levels for trivalent erbium.
23 November 2020 172 2 View
Is it possible to transfer heat from one group to another using simulated aneeling technique in the Gromacs software? I would like to transfer heat from a gold nanoparticle (group 1 from 310 to...
21 November 2020 9,365 3 View
Hello, I've been investigating a bunch of monomers which spontaneously react in water to form a polymer. I would like to know how to calculate the thermodynamics of such a system. On the surface,...
19 November 2020 5,830 3 View
hi I am trying to simulate electroporation for a bilayer containing 10% cholesterol on GROMACS. I have read lots of articles but the only parameter that they have talked about was the electric...
16 November 2020 7,813 2 View
I have a 500 ns molecular dynamics trajectory with several proteins in a membrane. The entire system is enclosed in a periodic box. Unfortunately, my proteins are only interacting around the...
12 November 2020 7,245 3 View
Dear Lammps/MD experts, I am going to model an epoxy resine structure with Lammps. The initial structure of epoxy resin (Epon resin 862) is available online in for example in CDXML format (as...
10 November 2020 1,367 3 View
Dear ceramics experts, I need to verify my MD simulation results with experiment. I have modeled compression behavior of TiO2-anatase nanoparticle (30/40 nm) under different crystallographic...
10 November 2020 6,603 4 View
I have 2 drugs with similar effect. They both INDIVIDUALLY showed a good docking using autodock. I am wondering if there is an MD approch to quantitate how those 2 drugs can have stronger binding...
30 October 2020 2,249 5 View