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Questions related to Molecular Dynamics Simulation
Are their any advantages of using mixture of two solvents rather than one solvent for exfoliation of 2D nanomaterials?
31 March 2023 2,053 2 View
I am facing this error while nvt simulation constantly i am done trying adding -dflexible flag using steep integrator during em also and nvt,mdp also,still error persists how to resolve it , i am...
29 March 2023 3,570 0 View
I am working on membrane lipids and am entirely new to the field. Currently, I am focusing on heart cell membranes. I need the exact composition of lipids present in the human myocardial membrane....
25 March 2023 4,033 2 View
I am currently using VASP, where I want the system to be charged. I add or remove electrons but due to the VASP artifact it adds the background charge to the system. I am looking for a way, where...
22 March 2023 4,326 1 View
Hello to all, I need to perform a standard curve for metagenomic analysis with qPCR, of Treponema Denticola and Pseudoramibacter Alactolyticous, using the 16S RNA copies of my DNA. As well I...
18 March 2023 805 3 View
I ran gromacs with command: grompp -f ions.mdp -c protein a_solv.gro -p topol.top -o ions.tpr. and yielded a Fatal error: number of coordinates in coordinate file (solv.gro, 57741)...
16 March 2023 7,039 1 View
I have successfully installed MGL tools 1.5.7 in windows 11. After the installation is finished, when I run "AutoDockTools" by double clicking the icons on the desktop, the windows command prompt...
16 March 2023 9,149 4 View
Hi every body. I want to do a MD in gromacs for protein but it have a non standard residue. Somone who tell me how I can to do it? Which programs I should to usage? or some tutorial that I can to...
15 March 2023 4,199 4 View
I am working on MD simulation of a nanocomposite .Based on some reactions ,I need to use reaxff forcefield for a better insight. But a force field file for B,N,Si,C,O elements is not available.I...
14 March 2023 4,085 3 View
How does a positive value indicate better binding energy for MM-PBSA binding free energy calculations?
12 March 2023 8,333 5 View
Hello I want to melt the polymer, but the viscosity of the polymer in the molten state is high. Is there a way to reduce the viscosity of the polymer melt (not the viscosity of the polymer solution)?
11 March 2023 5,293 5 View
Can anyone help me by explaining how the normal mode coordinates are written in Gaussian16 frequency calculations? I understand that they are normalized and hence can be considered "unitless"...
08 March 2023 4,118 3 View
These are the most controversial thesis of the famous physicist. Most of the community disagree but no official thesis yet (i m working on one) partly because no big journal published them. The...
05 March 2023 8,086 18 View
I want to retain crystallographic waters in protein structure while docking a ligand. How to prepare pdbqt file in Vina considering explicit waters? Also is there any modification required in the...
05 March 2023 2,172 2 View
I require the generation of peptide structures and computation of van der Waal interactions (1-4 interactions) from a given set of backbone Ramachandran angles, for fixed bond lengths and bond...
05 March 2023 3,016 5 View
I'm planning to do some molecular dynamic simulation with Gaussian, (trying to simulate the alignment of an ensemble of water molecules in the presence of strong field), can anyone please explain...
03 March 2023 2,176 3 View
I have made a membrane + protein system in Charmm gui can you give me methods to "how to do analysis on membrane protein computationaly?"
02 March 2023 5,025 4 View
My stock protein concentration is 2.13mg/ml. I have to have a final concentration of 0.83 nanomoles and my final volume for the protein would be 50 microlitres. The molecular weight of the protein...
01 March 2023 5,453 3 View
I have the output (-out.cms) file of the protein ligand simulation from Desmond. I wish to analyse some different aspects of the obtained Desmond output file in Gromacs. What are the necessary...
28 February 2023 9,728 0 View
How to prepare topology file for coordination (complex) compounds. Topology files for organic ligand molecules can be obtained using online servers such as SwissParam and etc. How to prepare a...
27 February 2023 3,945 1 View
I want to use cpptraj for some analysis but I need to convert my topology and trajectory files from Gromacs xtc, tpr format to Amber nc and parm formats. Could you please let me know how can I...
26 February 2023 3,000 2 View
I created a file af polycrystal diamond using atomsk and saved it using .lmp extension. When I run the file in lammps it is unable to read it but when I prepare a .lmp file for single crystal...
23 February 2023 2,002 3 View
I need to store a large amount of MD simulation trajectories in a database that I can interact with using python. Do databases like this exist currently?
22 February 2023 4,971 2 View
Hello, I am trying to apply a restraint between an atom in my ligand (atom number 12) and an atom in the active site of my protein (atom number 582) in GROMACS. I have modified the [ bonds ]...
16 February 2023 9,009 2 View