Categories
Tag: Lambdas
AWH very large free energy barriers – User discussions
Noob December 10, 2023, 12:43am 1 GROMACS version: 2023.3GROMACS modification: NoI have been trying to run a Free energy simulation using AWH and no matter what I set some of the values too I keep getting the same error: ——————————————————- Program: gmx mdrun, version 2023.3 Source file: src/gromacs/applied_forces/awh/pointstate.h (line 355)…
Automating API Documentation: A Journey from TypeScript to OpenAPI and Schema Governence with Optic
In the previous blog post Documenting and Testing Schemas of Serverless Stacks with Optic & Cypress, we focused on the benefits of schema testing and governance. Briefly, some of the core problems addressed were: Effortless API Documentation: Automating the API documentation creation and update, ensuring that our API documentation evolves…
Implausible values in free energy calculations – User discussions
alkosh November 14, 2023, 2:29pm 1 GROMACS version: gromacs-2022.4GROMACS modification: Yes/No Hello! I am trying to calculate the free energy of a ligand on the nanoparticle. While calculating NP-Ligand – NP-Dummy free energy I faced with a strange behaviour of gromacs: Detailed results in kT (see help for explanation): lam_A…
How to set-up three-step transformation path in FEP calculation in GROMACS mdp file – User discussions
GROMACS version: 2022.5GROMACS modification: No Hi, Everyone! I am new to FEP calculation and recently perform some FEP calculations of protein single mutation using GROMACS + pmx. In my benchmarks, the calculation details are listed below: Mutationala-scaning mutation(residue mutated to Ala) and normal mutation(residue mutated to other non-Ala residues) Transformation…
10 Engineering Jobs to Apply in Bangalore
Here are the top 10 engineering jobs you can consider applying in Bangalore Engineering is a dynamic field that plays a pivotal role in shaping the world around us. From designing cutting-edge technology to building infrastructure that facilitates our daily lives, engineers are at the forefront of innovation and progress….
System Exploding? – User discussions
oSalad August 25, 2023, 6:50am 1 GROMACS version: 2021GROMACS modification: NoHello,I am trying to convert an acid into its anion through the alchemical annihilation of the hydrogen. However, my system runs into this error and crashes at around 100ps /1000 ps when my lambdas are still 0: Fatal error:There are…
Gromacs: gmx::UpdateConstrainGpu::Impl Class Reference
#include <gromacs/mdlib/update_constrain_gpu_impl.h> Class with interfaces and data for GPU version of Update-Constraint. Impl (const t_inputrec &ir, const gmx_mtop_t &mtop, const DeviceContext &deviceContext, const DeviceStream &deviceStream, GpuEventSynchronizer *xUpdatedOnDevice, gmx_wallcycle *wcycle) Create Update-Constrain object. More… void integrate (GpuEventSynchronizer *fReadyOnDevice, real dt, bool updateVelocities, bool computeVirial, tensor virial, bool doTemperatureScaling,…
Step-by-step Migration Guide: From AWS API Gateway to KrakenD API Gateway
Introduction As you consider migrating from AWS API Gateway to KrakenD API Gateway, you’re likely driven by a number of compelling benefits such as a better pricing model, reduced vendor lock-in, operational simplicity, enhanced content manipulation and transformation capabilities, increased connectivity protocols, and extensibility trough Custom golang Plugins or Lua…
molecular polarizability calculated via cp2k is different from psi4 and gaussian09
I am trying to calculate molecular polarizability of a single CH4 molecular via cp2k software using the B3LYP functional and the d-aug-cc-pVDZ basis set. The strategy is as follows. By changing the polarization direction of the electric field, the corresponding molecular dipole moment is obtained, and then the molecular polarizability…
Free energy calculation of protein-ligand system – User discussions
GROMACS version: 2021.4GROMACS modification: Yes (PLUMED patch) I am trying to calculate free energy of a system where one ligand molecule is stuck inside protein fibril and one outside the fibril. The inner ligand’s vdw force becomes zero and the outer becomes a non-zero value over lambda steps.I have tried…
MDRUN crash during gREST simulation under NVT ensemble – User discussions
GROMACS version: 2022.3GROMACS modification: No Hello everyone. I am currently using GROMACS ver. 2022.3 patched with PLUMED ver. 2.8.1., and I’ve been trying to replicate the gREST simulations from Oshima et al. (J. Chem. Inf. Model. 2020, 60, 11, 5382–5394) using GROMACS. In the paper, the authors perform gREST simulation…
Error met in free energy calculation – User discussions
GROMACS version:2022.5GROMACS modification: NoI am trying to do free energy calculation on a protein-ligand system. I met such error when I doing the ligand part: There are perturbed non-bonded pair interactions beyond the pair-list cutoffof 1.26317 nm, which is not supported. This can happen because the system isunstable or because…
New England Journal of Medicine Publishes Positive Phase 3 TOGETHER Results with Peginterferon Lambda in COVID-19
– Phase 3 TOGETHER data showed early treatment with a single dose of peginterferon lambda (Lambda) in patients with mild-to-moderate COVID-19 infections resulted in significantly decreased clinical events – Lambda reduced risk of hospitalization or emergency room visits by 51% (primary endpoint) – Lambda reduced risk of hospitalization by 42%…