Questions tagged [molecular-dynamics]
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Generating 3D cartesian coordinates of a peptide and computing van der Waal interactions (1-4 atoms) for a given set of dihedral angles?
I wanted to generate 3D Cartesian coordinates of a peptide sequence for fixed bond lengths and bond angles for a given set of backbone dihedral angles and side dihedral angles. I also wanted to ...
Molecular dynamic simulation, reconstuction of protonation pattern of a protein from PDB file without resolvent hydrogen
I'm trying to build a topology of a protein using GROMACS. The pdb file do not include coordinates of hydrogen atoms. So I was wondering how to assign appropriate protonation states for each residue. ...
Energy minimization of molecules
I have 3000 molecules which I need for docking but before that I need to perform energy minimization for all the molecules and it is taking a long time because I am doing it one by one. So is there a ...
How to create an Alchem configuration file for NamD simulation?
I am trying to use NamD for Alchem simulation for a bilayer system. I am using the script below as the configuration file, but after the minimization step, I am getting this error: "FATAL ERROR: ...
Creating hybrid topology using VMD
I wanna create a Hybrid topology for alchemical free energy calculation. I am using the VMD plugin mutator to create that hybrid topology. But, I am facing this Error: unable to load structure file ...
Generating intercalation site in DNA for custom sequence
Thank you for your help. Can anybody please tell me how I can generate an intercalation site in DNA at the base pairs I am interested on. I appreciate if you can please guide me to any tutorials or ...
Drug-DNA complex simulation using AMBER
I want to carry out the simulation of drug-dna complex by placing the drug molecule at particular site in my DNA sequence (intercalating site). I have PDB files of both drug and DNA sequence. I will ...
GROMACS RMSF Result Analysis Problem
This is RMSF for protein from GROMACS after 100ns simulation- I have few questions- Residue numbers are starting from 1650 to 1850, has it ignore LIG and HOH as residues? There are three lines, so ...
Sending chimera MD to remote computer
I am using Terminal to try to run Chimera MD simulations on a remote server/computer. I have been able to successfully connect using the command ssh username@detroit05 (and then entering the password)....
How to make a video of a gromacs gmx dump standard output with VMD
I did gmx trjconv on GROMACS trr file to generate a .xtc file, and then used ...
Gromacs molecular dynamic simulation throwing error during minimization
I am trying to investigate a membrane proteins influence on a lipid bilayer using molecular dynamics. I am new to MD and trying to run my first simulation. I have built the simulation input files ...