Could I use swissparam provides topology and parameters for small organic molecules compatible with the Gromos96 53a6 force field?

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CYP2D6 MD simulation?

Im working on simulating a CYP2D6 with its cofactors (heme ) with GROMACS. When I run pdb2gmx, using CHARMM27 FF, I had no error.After looking in the literature, I found their corresponding...

07 August 2017 6,898 2 View

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

AUX gas reading problem on QE with full MS and PRM method in one run?

Dear QE-users, In the method where full MS positive mode and PRM mode are used, we always get an incorrect auxiliary gas reading (41 instead of 25). This only happens in this method; other...

06 August 2024 4,953 0 View

People weight in Oaxaca Blinder Decomposition on R?

Hello guys! Do you have experience running a Oaxaca-Blinder decomposition on R applying person weights. How do you suggest doing it? I have a variable PERWT which gives more information on how...

04 August 2024 6,033 0 View

Why don't d-orbitals split themselves, why does it take a ligand? why don't protons from ligand repel nucleus split d-orbitals?

why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...

03 August 2024 3,589 3 View

Why doesn't chromium 2+ ion use all its d-orbitals to receive lone pairs from six waters in [Cr(H20)6)]3+?

I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...

03 August 2024 1,370 1 View

How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer

30 July 2024 3,354 1 View

How to perform EEG source analysis on each trial of data separately?

Hello Everyone I have a question about structure for connectivity analysis on sources. My goal: preprocess and cut data into trials create headmodels, using template MRI file perform source...

30 July 2024 2,744 1 View

How to add Cr parameter in autodock?

When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!

29 July 2024 488 0 View

Why running a restart analysis in Abaqus in Ubuntu OS gives an error as attached when running the same job in Windows doesn't give any error and runs?

I am trying to run a restart analysis, which imports deformed configurations of parts from a generated ODB file. It runs fine in Windows OS but when I try to run it in Linux OS, it is giving some...

29 July 2024 9,572 3 View

How to use Desmond in HPC ?

Our department has recently acquired an HPC (High-Performance Computing) system, and I'm thrilled to take my molecular dynamics calculations to the next level using Desmond. I used to run my...

28 July 2024 6,553 1 View