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Questions related to Molecular Dynamics
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 3,297 2 View
In nvt.mdp file during protein-ligand complex MD Simulation, you have: title = Protein-ligand complex NVT equilibration define = -DPOSRES ; position restrain...
23 June 2020 7,233 1 View
GROMACS version: 2018.7 Running 3 mb GROMACS lysozyme tutorial simulation on high-performance computing server with GPU and final mdrun command keeps getting error of “not enough memory. Failure...
18 June 2020 951 1 View
I have obtained the J0Jt.dat file by Molecular Dynamics using the LAMMPS software. How can I obtain the curve for HCACF (heat current autocorrelation function)?
11 June 2020 6,249 1 View
If it happens that during your homology modelling and MD study of such protein, other authors published the x-ray crystallographic structure of the same protein. What should be done? can you...
11 June 2020 5,389 7 View
I am new to MD / gromacs and I am trying to use MD not for biological system but for generic materials science. Specifically, I am trying to simulate the interaction between hydrophobic molecules...
08 June 2020 9,115 2 View
07 June 2020 2,268 4 View
Hi, experts I want to predict an XRD pattern of a certain compound. I had optimize the crystal structure with ADF program. But the exported data in "cif" format is just xyz coordinates +...
11 May 2020 9,474 0 View
Dear all, I am currently in bioinformatics, as an undergraduate. In md simulation, I calculated binding free energy of protein-ligand complex model by MM/PBSA. As MM/PBSA method has some...
11 May 2020 2,019 4 View
Hi everyone! I am currently analyzing proteomics data as part of my master's thesis but I am struggling with the log transformation. I need to analyze iTRAQ LCMS data but I do not have the...
09 May 2020 218 0 View
If I have the chance to start with one of these two subjects, do you recommend starting with docking or dynamics?
08 May 2020 3,351 21 View
I want to simulate a niosome bilayer with schrodinger software (molecular dynamics), but first I have to design the proper bilayer. Does anyone know a software or simulator to design a bilayer...
06 May 2020 1,211 10 View
Hello everyone, I'm studding thermal properties of amorphous SiO2(a-SiO2) via molecular dynamics(LAMMPS) using Tersoff potential(Interatomic potential for Si–O systems using Tersoff...
05 May 2020 4,837 2 View
I am going to conduct molecular dynamics analysis of the protein-ligand complex in a Computer-Aided Drug Design project.
05 May 2020 7,369 3 View
Hi all, I have a couple of questions for PMF calculations in Gromacs. I placed a nanoparticle (NP) in the water region approximately 1nm away from the membrane and by using Gromacs pull code, I...
22 April 2020 3,960 4 View
I would like to ask for some advice for building a personal computer for general home use and bioinformatics (mainly molecular dynamics, like CUDA calculations in GROMACS, AMBER, ect) Budget is...
19 April 2020 4,155 0 View
Both beginning temp and target temp are 300 K. Why doesn't this reach 300 K? Please refer to picture that I attached INCAR file goes like this ENCUT = 400 NSW = 50000 IBRION = 0 ISIF = 2 LREAL...
07 April 2020 7,182 1 View
I performed a molecular dynamics in GROMACS 2019.2 of a protein with zinc fingers (50 amino acids). When I visualize it with Chimera the ions jump everywhere.
06 April 2020 9,546 7 View
FE is a widely acknowledged and popular tool for complex problems. However, computation at nano-scale is more complicated where strain or strain gradient may come at even smaller scale. Other...
30 March 2020 8,542 7 View
I want to compare the protein dynamics ) pH 7 versus pH 3, or ) wild type versus mutant The protein will have slightly different number of atoms at each condition, due to protonation or...
26 March 2020 3,942 3 View
Dear all, I am trying to calculate the number of water molecules at a distance of 0.35A from the protein. I used two gmx select GROMACS codes which have given me different answers. 1. gmx_mpi...
18 March 2020 9,299 3 View
I just wanted to know the Joint Committee on Powder Diffraction Standards (JCPDS) card number for silver nanoparticles and whether it can be called as JCPDS or ICDD?
12 March 2020 9,910 3 View
pdb files containing molecular structure coordinates to sdf format
12 March 2020 3,223 4 View
Hello! What is the recommended way to choose collective variables / reaction coordinates to study ligand binding to a protein (e.g., for PMF free energy profiling)? I often see the advice like "Do...
11 March 2020 2,012 4 View