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Questions related to Molecular Dynamics Simulation
Hello. I am trying to use gromacs to start an MD simulation of a protein-ligand complex. I was following the recommended tutorial http://www.mdtutorials.com/gmx/complex/index.html - I did the...
17 March 2022 6,303 4 View
Dear all, I'm a new user to apply a ReaxFF force field. Before I use it, I'm doing some tests of some simple systems. When I was doing a simulation of a Diamond system under NVT (actually under...
14 March 2022 4,549 5 View
Hello, How do you all normally analyze multiple MD simulation trajectories. For my system, I ran 5 100 ns simulations using an different initial velocity. Do you perform cluster analysis and then...
10 March 2022 6,975 3 View
When I use the DFTB theory of the cp2k package, I find that there is no potassium ion in the Slater-Koster parameters set (matsci), but I use the xtb method to test the potential function of mica,...
09 March 2022 1,104 5 View
I ran a molecular dynamics simulation for a system that consists of a peptide-protein complex, the binding happens at certain residues. on calculating the MM-GBSA per residue energy decomposition...
08 March 2022 8,096 4 View
Hello! I am currently doing an MD simulation with LAMMPS and calculating the interaction energy between two groups. However, the group/group command only gives the total interaction energy,...
08 March 2022 5,622 3 View
I have been working on the design of covalent inhibitors, which are covalently bound to the cysteine side chain. it would be really helpful if somebody would guide how to modify the processed...
07 March 2022 6,755 3 View
I am going to calculate the free binding energy of two proteins which are in a complex. I have used the umbrella sampling for this purpose, but after pulling, the two proteins do not separate...
07 March 2022 2,033 5 View
How can we calculate rmsf value of protein-ligand complex in md simulation of protein-ligand complex in gromacs? What would be its significance in case md of drug-protein complex? What other...
04 March 2022 5,555 2 View
i have been doing the molecular dynamic simulation for 6lu7 protein and some ligands and constantly getting the namd2 error.
04 March 2022 9,105 2 View
There is an option in prime mmgbsa panel of selection of protein flexibility, when I used it the results had turned negative. Any help?!
04 March 2022 7,075 1 View
I want to make a ZnO nanowire to perform MD simulation using lammps. I would like to know if there is an open source software that can build ZnO nanowire or is there other way to make such...
02 March 2022 8,559 3 View
I have to simulate carbohydrate-protein complex on GROMACS. I have used GLYCAM webserver to generate a trisaccharide. Then I used acpype of Ambertools21 to prepare carbohydrate ligand using...
01 March 2022 5,940 6 View
Dear all, Sorry for not being able to describe my question properly in the title. I just finished 100 ns simulation with GROMACS for my molecule, and I visualized the trajectory in VMD. The input...
01 March 2022 4,074 6 View
In the step of RMSD calculation using VMD, I have two gro file : one is energy minimized (em.gro) before I stared the remd simulation and another output file.gro which was generated after...
27 February 2022 5,248 4 View
I need to run molecular dynamic simulation for a protein-protein complex which i obtain from HADDOCK server. Are there any web servers which i can run md simulation? If yes ,could anyone suggest...
26 February 2022 9,455 4 View
I need to confirm the convergence of REMD simulation within 200 ns per replica so how can I calculate RMSD values with their corresponding free energy in equal-length non-overlapping time windows...
23 February 2022 9,839 1 View
I generated the complex of my protein and ligand and visualise it in Chimera and other visualisation software but I observed no interaction between my protein and ligand. What could be the cause...
22 February 2022 5,431 3 View
I need to find the converged conformational sampling within 200 ns per replica between RMSD and free energy in equal non-overlapping time windows like in the following graph?
21 February 2022 4,939 2 View
Why is my protein topol.top file like this? attached is the file
20 February 2022 6,823 4 View
Hello everyone. I have completed MD simulation for a macromolecule with 130 residues. after completion of the process, I found most of the residues of protein remain below 2.4 A. so can I say that...
18 February 2022 6,607 4 View
how can I fix this error in gromacs, ERROR 37 [file ligand.prm, line 41]: Incorrect number of atomtypes for dihedral (0 instead of 2 or 4)?
16 February 2022 4,104 2 View
Hi everyone, I have a doubt regarding the high negative average pressure values in MD. The prepared system was minimized (NVT ensemble) with 10ns using DESMOND software. While doing Simulation...
14 February 2022 7,006 5 View
How can I use ignh to ignore water molecules in a gromacs molecular dynamic simulation?
12 February 2022 7,764 1 View