How can I model a hexagonal phase using Packmol?

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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 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

How can we convert pdb structure to Gromacs when it contains DNA?

I want to convert the pdb format of topoisomerase I into Gromacs.The pdb id for the structure is 1K4T. I removed ligands, water and Hg ion from 1K4T. But DNA is required for the MD simulation. I...

08 September 2015 5,156 1 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 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

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 781 1 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View