Tag: VMD

Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster in , for Cedars-Sinai Medical Center

Details Posted: 26-Apr-22 Location: Nationwide Type: Full-time Salary: Open Internal Number: 20002022 At Cedars-Sinai, postdoctoral scientists and other junior researchers fulfill a critical role in expanding the horizons of medical knowledge through biomedical research. By hosting more than 100 postdocs, who conduct vital research and receive advanced training with expert…

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[lammps-users] How to define virtual atoms in the lammps? – LAMMPS Mailing List Mirror

Dear LAMMPS users, I need to build a molecule having a virtual atoms for the lone pair on the specific atoms. I made lammps data file and ran simulation. But it crashes at the beginning of the simulation. The error message says “Cannot compute PPPM”. I think this is because…

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how to create temporary folders in a slurm script hpc script code example

Example: how to create temporary folders in a slurm script hpc script #!/bin/bash #SBATCH –job-name=sand_min #SBATCH -N 1 #SBATCH -n 1 ##SBATCH –gres=gpu:1 #SBATCH –partition=shortq7 #SBATCH –exclude=node[007,041,046],nodeamd[010-014],nodeeng[009-010],nodegpu001,nodenviv[100001-100002,100004-100015] #SBATCH –mail-type=ALL #SBATCH –time=6:00:00 echo “NODE NAMES = “$SLURM_NODELIST echo “CUDA_VISIBLE_DEVICES = “$CUDA_VISIBLE_DEVICES date # # Load the necessary modules, etc… # module…

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LAMMPS fix print function – Stack Overflow

First of all, I’m very new to LAMMPS so I’m sorry if my question is trivial.I’m trying to model a gas of atoms that float in a square box, they obey an NVE integration and only feel a shifted Lennard-Jones potential, no other interaction is introduced. What I’m trying to…

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[lammps-users] Pyrolysis – LAMMPS Mailing List Mirror

Dear all, I hope you feel great. I have two questions: 1- I pyrolysis a box consisting of 10 chains of polymer, and for this purpose, I used the Reax-FF. After pyrolysis, I want to know which molecules and how many of them are produced. Could you please suggest tools…

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Has anybody used RIP-MD tool for generation of RIN from MD trajectories?

Has anybody used RIP-MD tool for generation of RIN from MD trajectories? 0 I have been trying to use the RIP-MD tool for generating residue interaction networks from pdb file and MD trajectories. I have tried installing the VMD plugin and running the files through that for the same. But…

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Extracting coordinates of possibly H bonded solvent molecule using BioPython

Extracting coordinates of possibly H bonded solvent molecule using BioPython 0 Hi, I am trying to extract the coordinates of solvent molecule from a peptide PDB, within a distance of 3 ang of O and N atoms in peptide. Using VMD, I can extract up to 3 ang of peptide….

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lib · lammps

This directory contains libraries that can be linked to when building LAMMPS, if particular packages are included in the LAMMPS build. Most of these directories contain code for the library; some contain a Makefile.lammps file that points to where the library is installed elsewhere on your system. In either case,…

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Advise for a computational neophyte

Forum:Advise for a computational neophyte 0 Hello, biostars! Once I have earned B.Sc. in Biotechnology (in Russia it’s a pretty weird combination of biology, engineering and almost all branches of chemistry), turned to a bigger city to gain a M.Sc. degree. In our research lab we have 2 professors for…

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