Categories
Tag: VMD
Division of the box into smaller regions – LAMMPS General Discussion
Hi, I’d like to divide my simulation box into smaller boxes (regions).Specifically, I want to have 24 smaller boxes on each axis (24x24x24). In the region command, apart from defining the boundaries of each region separately, is there any faster way to divide the cell into 24 regions on each…
How to generate topology for Graphene molecule from .gro file using GROMACS program? – User discussions
vikas28 December 18, 2023, 11:31am 1 GROMACS version: GROMACS/2022.4-fosscuda-2020bGROMACS modification: Yes/NoHere post your questionGreetings, everybody. I have generated a graphene sheet using the VMD program and saved the resulting file in the .gro format. Now I would like to use the GROMACS program to model the interaction between graphene and…
How to group atoms as molecules in reax – LAMMPS General Discussion
Using Aug 2023 version of Lammps This is a rather basic issue. I am following the paper by Kim to model , water, ethahol and phosphoric acid adsorbed to TiO2 using their ff.Reactive MD-force field: Kim, S.-Y., van Duin, A. C. T., and Kubicki, J. D., 2012, Molecular dynamics simulations…
Seeking In-Depth Advice: Drawing Lammps MD Simulation with VMD, Avogadro, or Alternatives – LAMMPS
Hello, community! I’m currently working on a molecular dynamics (MD) simulation using LAMMPS, and I’m looking for comprehensive guidance on visualizing and drawing the simulation results. Specifically, I’m interested in using VMD, Avogadro, or any other software that you would recommend. I’ve attached an example image of my simulation results…
Is it important to repeat analysis – User discussions
pelinsu November 22, 2023, 7:27pm 1 GROMACS version:GROMACS modification: Yes/NoHere post your questionIs it important to repeat the simulation? My RMSD values are quite good and the VMD movie is successful. Extra SASA, RMSF, protein-ligand interaction analysis was performed. But is it still important to do 3 repetitions? for publication…
DNA molecular dynamic trouble – User discussions
GROMACS version: 2023.3GROMACS modification: NoHi everyone!I have problems with DNA modeling. During molecular dynamics, DNA loses nucleotide bonds. Upon closer examination, literally one connection is missing. It disappears during the molecular dynamics ensemble.Does anyone know what could be wrong? I still can’t determine the reason. Maybe it’s something to do…
Change topology from GAFF to REAXff – LAMMPS Beginners
yel21 October 31, 2023, 9:04am 1 Hi LAMMPS users, I have simulated the mechanical and thermal physical properties of the different polymers using the GAFF force field at different temperatures below and close to the glassy state. However, in the classical force field, it is impossible to simulate the deformation…
How to get PDB file from lammpstrj files – LAMMPS General Discussion
Hi All, I have generated the LAMMPS data file using the CA atom coordinate of the PDB file, run the LAMMPS simulation, and got the lammpstrj file. now, I have the last snapshot of the trajectory file and try to generate the PDB file.Is it possible to get the PDB…
Convert PROCREATE to SAM
Popular conversions of PROCREATE file Converthelper.net is free tool to use, and we have 100.000 of conversions daily. Here is latest conversions from PROCREATE file on our servers: PROCREATE to WBC, PROCREATE to SYX, PROCREATE to ETF, PROCREATE to UNAUTH, PROCREATE to WMA, PROCREATE to CDMTZ, PROCREATE to PNT, PROCREATE…
Structure of human TRPM8 channel
Reagents and chemicals pFastBac Dual His6 MBP N10 TEV LIC cloning vector (5 C) was purchased from Addgene (Addgene plasmid no. 30123; www.addgene.org/30123). All restriction enzymes, the pFastBac1 vector, and DH10Bac cells were purchased from Thermo Fisher Scientific. Sf9 cells were purchased from ATCC. Q5® High-Fidelity DNA Polymerase, the Monarch® DNA…
Gmx trjcat not splitting trajectories – User discussions
GROMACS version: 2021.5GROMACS modification: No Hello everyone,I’m posting this so maybe somebody can help me with my issue.I’m using a trajectory that is about 120 us long, representing various folded and unfolded states of a protein.I used MDAnalysis and RMSD to discriminate between the folded and the unfolded states and…
Problem for gmx trjconv – User discussions
Wentao October 5, 2023, 5:52am 1 GROMACS version: 2023.1GROMACS modification: Yes/No When I use gmx trjconv to remove pbc and rot+trans on a trajectory, the new xtc trajectory shows a sudden dramatic shift in the atomic coordinates of some frames. To put it figuratively, imagine a movie where a person…
Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster in , CA for Cedars-Sinai Medical Center
Details Posted: 23-Sep-23 Location: California Type: Full-time Salary: Open Categories: Staff/Administrative Internal Number: 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…
Creating molecule file for lammps to simulate molecule deposition via deposit command – LAMMPS General Discussion
Can any one pls guide me through creating a molecule file for lammps deposition. I a constantly facing error stating “invalid header keyword -atoms” The file format is described in detail in the molecule command documentation. You just have to follow it exactly. Also, there are example files to compare…
Dcd file and VMD
Dear Cp2k developers, I use FIST on Cp2k version 2.0.0, with a system in a monoclinic cell that I specify by giving the three vectors A,B and C. Indeed, in the output I get INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02 0.1199999E+03 The corresponding .dcd file contains in the array cell(6) only the diagonal part of…
lammps – How to remove bonds between specific atoms in VMD
lammps – How to remove bonds between specific atoms in VMD – Matter Modeling Stack Exchange …
Non-Periodic system WARNINGS.
Dear all, I want to run a AIMD calculation in cp2k. I have prepared a box using packmol consisting of my system and 104 water molecules with cubic size of 15.1 x 15.1 x 15.1. And I want the my system to be in the center. It is a non-periodic…
Running Gromacs on CCAST Clusters
Introduction This document describes basic usage of GROMACS on CCAST clusters. Far more information about GROMACS is available in the GROMACS manual, which is available online and is maintained by the GROMACS developers. GROMACS is a free and open-source high-performance molecular dynamics package, mainly designed for simulations of proteins, lipids,…
Postdoctoral Scientist – Jones Lab
Details Posted: 10-Aug-23 Location: Los Angeles, California Type: Full-time Salary: Open Internal Number: HRC1341107 Principal Investigator, Michelle Jones, PhD, is looking for a Postdoctoral Scientist to join her lab! The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group established in 2016, with the common…
Cedars-Sinai hiring Postdoctoral Scientist – Jones Lab – Center for Bioinformatics and Functional Genomics in Los Angeles, California, United States
OverviewCedars-Sinai is a hub for biomedical research and a training center for future physicians and other healthcare professionals. By joining us in an academic role, you’ll be a part of formulating future ideas for discovery and then translating those discoveries into cures for the benefit and health of the Los…
29 Biorender Alternatives 2023-Find Out Which One Suits You The Best!
Biorender is a popular site used by students, professionals, and hobbyists alike. It offers an easy way to create diagrams on the basis of given data or figures. However, there are some alternatives available that can provide similar functionality or even better application features than what biorender has to offer….
Query Regarding Visualization of PBC Behavior in CP2K AIMD Simulation
I hope this email finds you well. I have a query regarding my CP2K AIMD simulation involving a water box with periodic boundary conditions (PBC) in the XY direction. Here is an excerpt from my input file: &CELL ABC 24.4797 24.4797 200.0 ALPHA_BETA_GAMMA…
Unexpected 0D wavelet errors at large vacuum
Hi it works for me (CP2K Trunk version) Precond_solver : DEFAULT stepsize : 0.08000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ———————————– OT ————————————— Step Update method Time Convergence Total energy Change —————————————————————————— 1 OT DIIS 0.80E-01 7.1 0.10459074 -83.0126092838 -8.30E+01 2 OT DIIS 0.80E-01 7.0 0.07934045 -85.4719301173 -2.46E+00 3 OT DIIS 0.80E-01 7.3 0.04237559…
CEDARS-SINAI Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster in Sacramento, CA | 850340891
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 …
Differential interactions of selected phytocannabinoids with CYP2D6 polymorphisms
Phytocannabinoids (pCBs) refer to compounds from the cannabis plant (Cannabis sativa), also known as cannabinoids , we found that pCBs can be differentially metabolized by different cytochrome P450 (CYP) and different polymorphisms of human CYP2D6, In addition, inhibition or activation of enzymes involved in drug metabolism by pCB will in…
Gromacs: Interactive molecular dynamics (IMD)
This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Allows mdrun to interface with VMD via the interactive molecular dynamics (IMD) protocol. Author Martin Hoefling, Carsten Kutzner ckutz.nosp@m.ne@g.nosp@m.wdg.d.nosp@m.e file imd.cpp Implements functions of imd.h. file imd.h This file contains…
Confusion reagrding the definition of major,middle and minor axes in gmx_principal – User discussions
psur June 21, 2023, 7:38am 1 GROMACS version:2022.1GROMACS modification: No I have calculated moment of inertia (m.o.i) around each principal axes using gmx_principal. In the GROMACS manual it is written that first principal axis is the major axis and there are middle and minor axis next. What is the definition…
CEDARS-SINAI Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster in Los Angeles, CA | 847542671
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 …
Class B1 GPCR activation by an intracellular agonist
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…
A Beginner’s Guide to Perform Molecular Dynamics Simulation of a Membrane Protein using GROMACS — GROMACS tutorials https://tutorials.gromacs.org documentation
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…
CEDARS-SINAI Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster in Sacramento, CA | 844690591
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 …
Periodic Boundary Conditions Error, Molecule Trajectory Collapses to 2D – User discussions
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…
[gmx-users] about dumping the last frame
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…
CEDARS-SINAI Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster in Sacramento, CA | 839444399
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 …
Ligand_ini.pdb is forming a distorted structure of ligand after running python script – User discussions
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 – Bioinformatics Research Scientists – Beverly Hills, CA
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…
Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Clusterother related Employment listings
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…
Trajectory shows long lines during VMD visualization – User discussions
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…
Pull_f and Pull_X graphs showing sharp peaks – User discussions
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…
Lammps fix bond/react unable to visualize the polymer chains – LAMMPS Beginners
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…
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS | BMC Bioinformatics
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…
Trjconv jumping DNA – User discussions
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…
Simulating/analyzing new shape/structure in VMD and LAMMPS – LAMMPS General Discussion
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,…
Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation
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…
Extracting itp of a fragment from a bigger structure – User discussions
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…
Structural basis for bacterial energy extraction from atmospheric hydrogen
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…
Input file for GCMC simulation using Lammps – LAMMPS General Discussion
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…
Coarse-grained simulation of RNA using LAMMPS – LAMMPS Beginners
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…
Does the .gro file matter? – User discussions
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…
Page Not Found – Materials Science Community Discourse
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…
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 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 …
Periodic and non-periodic box
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…
Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster at Cedars-Sinai
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…
How Build a Nanotubes by Uncommen Atoms? – LAMMPS
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.)…
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…
[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…
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…
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…
[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…
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…
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….
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,…
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…