Tag: VMD

Expression and purification of human PTH1R The plasmid encoding human PTH1R (GenBank identifier: U17418.1; residues 27–491) was constructed and purified as previously reported17. The construct was expressed in HEK293 GnTI (N-acetylglucosaminyltransferase I-negative) cells (American Type Culture Collection, CRL-3022) using the BacMam system (Thermo Fisher Scientific), and the cells were grown…

Building the protein-membrane system in CHARMM-GUI We are now ready to embed the protein structure in the membrane in the proper location and orientation and construct the membrane composition we desire. To do this, we utilized the CHARMM-GUI input Generator, a handy web-based tool to generate GROMACS inputs for the…

At Cedars-Sinai,postdoctoral scientists and other junior researchers fulfill a critical role inexpanding the horizons of medical knowledge through biomedical research. Byhosting more than 100 postdocs, who conduct vital research and receive advancedtraining with expert faculty mentors, Cedars-Sinai supports theongoing medical education process that continues beyond PhD/MD graduation.   Overview: Bioinformaticsand Integrative Genomics  …

GROMACS version: 2020.4GROMACS modification: No I have been running simulations of small proteins in water. Nothing fancy. Have been doing them without a hitch for awhile now. This last one I tried to do, however, behaved very strangely. The simulation seems to run for 125ns without any problems, but when…

Post by nahren manuelDear Awasthi,go through GROMACS Introductory tutorial…trjconv -f abc.pdb -s abc.tpr -o 3frame.pdb -dump 3You can also open the pdb file in VMD and save only the last frameSIMPLE !nahrenFrom: Shirin Awasthi Subject: [gmx-users] about dumping the last frameTo: gmx-users at gromacs.orgDate: Monday, February 2, 2009, 12:00 PMHi.I…

At Cedars-Sinai,postdoctoral scientists and other junior researchers fulfill a critical role inexpanding the horizons of medical knowledge through biomedical research. Byhosting more than 100 postdocs, who conduct vital research and receive advancedtraining with expert faculty mentors, Cedars-Sinai supports theongoing medical education process that continues beyond PhD/MD graduation.   Overview: Bioinformaticsand Integrative Genomics  …

Amey May 3, 2023, 10:42am 1 GROMACS version:2022.4Dear all,I am Trying to run ligand-protein complex MD simulation in GROMACS. My ligand_ini.pdb and ligand.gro files are not generating properly.After running of python script downloaded from MacKerell lab website a file is generated: ligand_ini.pdb. After viewing it in VMD it does not…

Cedars-Sinai Posted Under: Beverly Hills, California jobs in Other; Other jobs in zipcode 90213 Posted On: 2023-04-08 Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster At -Cedars-Sinai,postdoctoral scientists and other junior researchers fulfill a critical role inexpanding the horizons of medical knowledge through biomedical research. Byhosting more than 100…

At Cedars-Sinai,postdoctoral scientists and other junior researchers fulfill a critical role inexpanding the horizons of medical knowledge through biomedical research. Byhosting more than 100 postdocs, who conduct vital research and receive advancedtraining with expert faculty mentors, Cedars-Sinai supports theongoing medical education process that continues beyond PhD/MD graduation. Overview:Bioinformaticsand Integrative Genomics…

GROMACS version:2023GROMACS modification: Yes/NoHere post your question I have simulated a small RNA molecule for 1 us. This is a snapshot of the VMD visualization of the trajcectory of the molecule : I corrected periodicity effect using the following:gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC_whole.xtc -pbc wholegmx trjconv -s…

GROMACS version: Simulation using GROMACS 2022 w/ MPI and CUDA, all else 5.1.4GROMACS modification: NoI have been running some pulling simulations, but keep getting a strange artifact. Every once in a while (a few times per ns) the force jumps as the distance spikes down, causing an artificial unfolding. From…

Dev March 28, 2023, 6:07pm 1 I ran an example input file “in.tiny_polystyrene.stabilized’ located in a directory examples/PACKAGES/reaction/tiny_polystyrene shipped with Lammps version 8Feb2023The log file shows that the system has reacted with reaction values for f_rxn[1], f_rxn[2] and f_rxn[3]. When visualizing the trajectory, I was hoping to see some polyester…

The Molecular Dynamics (MD) is one of the techniques incorporated into bioinformatics, specifically by structural bioinformatics. With that, it is possible to obtain kinetic and thermodynamic characteristics of biomolecular structures. For example, macromolecular stability, identification of allosteric sites, elucidation of mechanisms of enzymatic activity, molecular recognition and properties of complexes…

GROMACS version:GROMACS modification: Yes/NoHere post your question Hi!I am currently facing a problem with erasing jumps from my system.I have tried several different combinations of the trjconv command which worked for other systems I have made, but not for my current system.I first tried only -pbc mol which worked fine…

I have a new structure that I want to analyze (lets just call it a shape). For the shape, I have the coordinates that make it up. I even have a tcl script in VMD that allows me to create the shape using graphics (draw triangle and draw lines). However,…

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021). Article  ADS  CAS  PubMed  PubMed Central  Google…

GROMACS version: 2021.3GROMACS modification: NoHere post your question I have gro and itp files for a really BIG 3D network (>100K atoms). Using VMD, I can extract coordinates of a smaller fragment (~2K atoms) in a gro file but wondering how to extract an itp also. I even tried extracting…

Statistics and reproducibility Huc purification and PAGE analysis Huc was purified from M. smegmatis cells on eight separate occasions throughout the course of the study. The yield of purified Huc (mg per litre of culture) varied by a factor of five between purifications. The relative abundance of the Huc oligomer…

I am trying to simulate the adsorption of H2s and Nh3 gas with a cof adosrbent. I have prepared the lammps data file using VMD Tk console for Adsorbent and the adsorbate gases. I am having problems while writing input file for the desired simulation.I am having trouble while grouping…

Hello everyone, I want to analyse a coarse-grained system of 2 RNA strands using LAMMPS.I was working with Gromacs and Martini coarse graining before, but since I did not get sufficient results I am looking for a program that allows for long (microsecond and longer) simulation times of coarse grained…

oSalad January 27, 2023, 4:44pm #1 GROMACS version: 2018GROMACS modification: No Hello,After solvation, energy minimization, equilibration, and running the production MD I get a .gro file. After looking at the contents of the .gro file, it just seems to hold coordinates. Are these gro files all the same thing or…

Sign Up Log In Log In Popular Nearest neighbours information at simulation timeLAMMPS General Discussion Abnormal force of NVE ensembleLAMMPS General Discussion Temperature was not constant but increased in NVE simulation with TIP4P/Ice modelLAMMPS Beginners Bond atoms 13 14 missing on proc 0 with FENE potential in a polymerLAMMPS General…

At Cedars-Sinai,postdoctoral scientists and other junior researchers fulfill a critical role inexpanding the horizons of medical knowledge through biomedical research. Byhosting more than 100 postdocs, who conduct vital research and receive advancedtraining with expert faculty mentors, Cedars-Sinai supports theongoing medical education process that continues beyond PhD/MD graduation.   Overview: Bioinformaticsand Integrative Genomics  …

 I’m new in CP2K and my question are: 1) Is there any way to print out the xyz file with the molecules ordered inside the box because every time I run, it always print out in an unordered way and to make it ordered I have to wrap it via…

Responsibilities Requisition # 20002022A 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 faculty mentors, Cedars-Sinai supports the ongoing medical education process that continues…

Here are some open sources that my friends and I find to model a “Nanotube” TubeGen Online – v3.4 Nanotube Modeler Software Materials Studio Software(OK, this one not free but it’s so practical) + Atomsk tool(in Linux) Edit plugins by tcl programming language for VMD(It’s free but very time consuming.)…

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…

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…

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…

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…

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…

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…

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….

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,…

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…