How can I visualize pdb structures gererated in MD simulations?

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How do we do micelle clustering and how do we make index file for molecules in micelles?

My system contains three micelles. I want to calculate radius of gyration for each micelle in the system. I did the micelle clustering, but I am struggling with the step 3 in...

07 August 2018 2,688 1 View

How can I model a hexagonal phase using Packmol?

Dear All, I want to arrange my surfactant molecules in a hexagonal arrangement for my MD simulation. Appreciate, if anyone can guide me to do that. Thank you.

06 July 2018 8,473 2 View

How to solve the Gaussian error; Water molecule starting at atom 93528 can not be settled?

Dear All, My system contains water molecules and polyethylene glycol molecules. I generated the box (15.2*15.2*15.2 nm*3) using genbox command. Thereafter, PEG molecules were added using gmx...

09 October 2017 7,114 0 View

What should I assign to pcon and ncon in polar.mdp in g_mmpbsa?

Dear All, In my MD simulation I only added counter ions (20 Na+ ions) to neutralize the system. Now I want to do MM_PBSA calculations for my MD runs using g_mmpbsa. In order to do perform polar...

06 July 2016 7,592 1 View

How to get publication quality images in PoseView?

Dear All, I want to get high quality images of 2D pictures generated by PoseView software. Can anyone help me? Thank you.

05 June 2016 6,174 1 View

Can we do molecular docking in the presence of crystallized water molecules using DOCK6?

Dear All, I want to do molecular docking processes for an enzyme and ligands in the presence of co-crystallized water molecules (of the enzyme) using DOCK6. Can anyone help me? Appreciate if...

05 June 2016 2,657 0 View

How rmsf of linker doamin in human topoisomerase I change with the binding ligand?

Dear All, I completed molecular dynamics for three ligands, T1L25, T2L25 and T3L25 using GROMACS software with CHARMM27 force field. How can I explain the rmsf behavior of linker domain (linker...

03 April 2016 5,142 5 View

Ligand interactions with DNA

Dear All, I have two receptor-ligand complexes. In one system, the ligand intercalates in DNA and from two hydrogen bonds (one with the enzyme and one with DNA duplex). In other system, the ligand...

02 March 2016 373 4 View

How can I use the itp file generated from SwissParm for MD simulation using GROMACS?

Dear All, I used SwissParm to generate CHARMM itp files for my ligand molecules. I used GROMACS for molecular dynamics simulations. After getting the itp file for the ligand, I used that file...

11 December 2015 3,653 0 View

How can I get topology file for my ligand molecule?

Dear all, Currently I am trying to do molecular dynamics simulations for human topoisomerase I enzyme. I am using GROMACS software with CHARMM forece field. I want topology file for my ligand...

10 November 2015 6,721 2 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 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

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 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 to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View