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Questions related to Molecular Dynamics Simulation
I would like to know why the system is equilibrated at 10 K with NVT and followed with 300 K with the NPT method while performing MD simulations. Please, provide available references.
11 February 2022 9,630 3 View
Why do I get high negative pressure values at the NVT ensemble step with 10 ns at 10 K temperature, and the pressure increases to single-digit positive pressure values at the NPT ensemble step...
11 February 2022 899 1 View
I doing MD simulation of protein-ligand interaction at two different temperatures 273K & 310K, how can I do this?
09 February 2022 632 4 View
Molecular Dynamic (MD) simulation for fluid-fluid or fluid-rock interaction process is not a new thing though, but only few have thought about this in case of mineral processing. I want to work...
08 February 2022 3,137 1 View
Hello, I need to check which water molecules (MD simulations) with their specific water IDs are coming at the catalytic pocket of my protein within hydrogen bond distance in 500 frames, i.e., in...
31 January 2022 8,757 2 View
Hi all, I have used the below code for analyzing hbonds in my protein, but I am facing the error below. Please provide solution for this error? python3 readHBmap.py -hbm hbmap.xpm -hbn rg.ndx -f...
27 January 2022 7,138 5 View
Dear scientific community members I am facing a problem in running a residue based coarse grain MD simulation. As we provide the minimization commands, it terminated with the error message Reason:...
27 January 2022 4,649 6 View
I was trying to do docking study with some proteins like 6LU7, 6W79 in Autodock. But every time in the time of running AutoDock after the AutoGrid, this error message is coming "error: 2137...
27 January 2022 9,351 4 View
Dear all, Can anyone support me to get the accurate .hbd entry for the "HA'' hydrogen in the attached molecule? My following entry gives an error in Gromacs I also want to know the "-C" meaning in...
26 January 2022 3,173 2 View
I faced a FATAL error while preparing Docked Proteins for MD simulation using Amber20. But this error does not occur while performing with non-docked protein structures. Is this problem is due to...
05 January 2022 1,711 3 View
Dear Research colleagues, Kindly help me in getting the structure of Functionalised MWCNT structure as MOL or PDB or SDF file format.
25 December 2021 5,548 0 View
Dear all, I have been trying to perform an MD simulation using Gomacs. My system has two ligands in DMSO solvent. While performing the NPT equilibration , I'm getting the following : Fatal error...
20 December 2021 3,757 3 View
I am interested to see the effects of electric field on the band structure of a 2D material. For this, first I did the atomic relaxation without an electric field. Then I added the electric field...
04 December 2021 1,190 1 View
I have a mixture of DMF and water in 300 K simulated with an OPLS-AA force field. The hydrogen bonds between oxygen atoms of DMF and H atoms of water have a very short length and it's around 1.26...
22 November 2021 2,635 3 View
I'm attempting to reproduce the bandstructure of LaFeAsO from Ref [1], Fig 2; as well as the much simpler FeSe. I expect (from experiments and published DFT results, i.e [1]) the bands...
09 November 2021 6,075 2 View
I am doing optical calculation for an quasi 2D perovskite with 188 atoms using SIESTA. I previously optimize the atom positions and later optimize the cell parameters too. The calculations of PDOS...
06 November 2021 6,888 0 View
Hello Everyone: Currently I am working on atomistic modelling of grain boundaries defects in CNTs therefore, I require a polycrystalline CNT. I have generated a polycrystalline graphene sheet...
27 October 2021 3,764 6 View
I am conducting a protein-docking analysis (in AutoDock Vina) and was asked about the use of a negative control. However if any there are only a handful of articles that have used negative controls.
15 October 2021 7,879 3 View
Hi, is there any type of method software tool, by which we can perform the normal mode analysis of the protein? If some have the tutorial then please let me know. Thanks.
13 October 2021 5,784 6 View
Dear All Can I place a peristaltic pump system with tubings and microfluidics chip completely into the incubator for 1-2 days long experiment? If yes, is there a specific brand for that...
06 September 2021 965 11 View
I have docked numerous ligands into my protein of interest, I would like to know how I can calculate the binding affinities between protein and ligands, or alternatively, how can the docking...
27 July 2021 4,184 3 View
Hi there. I'm a beginner of QM/MM and been trying to run ONIOM calculations. I ran the calculation and got output file as well . However, i don't know how to interpret the data. It looks almost...
09 July 2021 2,667 3 View
I need to do some modifications in a set of 20k PDB files for the same complex (solutions of Brownian dynamics) so that they are suitable for runnig some calculations in a NMR prediction program....
21 May 2021 2,464 4 View
i'm trying to run autodock, this series of warnings and an error popped any ideas C:/modelado_molecular/autogrid4.exe: WARNING: Found an H-bonding atom with three bonded atoms, atom serial...
13 May 2021 9,733 3 View