Critical points for methanol OPLS-AA?

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embedded-atom method (EAM) potential and "upper limit" "lower limit"?

Hi how set "upper limit" "lower limit" in embedded-atom method (EAM) potential? Thank you

31 December 2016 9,893 1 View

How can I change of protein's primary structure by molecular dynamic simulation?

I work on the interaction of CNT and proteins. The results show that the tertiary and secondary structure of proteins are changed (effected by CNT). VMD sequence viewer shows that the primary...

07 August 2014 5,880 2 View

Why am I experiencing protein unfolding, and why are the number of H bonds increasing?

I work with gromacs code on the protein carbon nanotubes interaction. I saw that when the protein becomes unfolded, the number of hydrogen bonds (in protein itself, not with water molecules)...

07 August 2014 5,623 2 View

What is the number of h bond per molecule in EG?

I need to know the number of h bond per molecule for ethylene glycol.

05 June 2014 3,632 1 View

Interaction between metal nanoparticle and protein?

Do you see any papers related to molecular dynamics simulation of metal nanoparticle and protein?

01 February 2014 9,242 0 View

Deviation from Raoult's law in methanol water mixture?

I see that in some papers the reported methanol-water in 300K shows a positive deviation from Raoult's law, but at low temperatures have negative deviation from Raoult's law. Does anyone have a...

10 November 2013 8,857 4 View

Is it possible to determine boiling point by lindemann index?

Is it possible to determine boiling point by lindemann index? I see some references, that work on melting point by lindemann index. But I need to determine boiling point by lindemann index.

10 November 2013 7,032 4 View

Is it possible prediction Raoult's law by MD?

Molecular simulation and Raoult's law.

10 November 2013 1,584 5 View

Hydrogen bonding and water methanol mixture?

I want to know that in methanol/water mixture from water rich to methanol rich, how change total hydrogen bonding in mixture? Less than pure water or not?

10 November 2013 4,015 6 View

Heat capacity and DL_POLY?

I need to calculate heat capacity from r.m.s fluctuation energy that reported in OUTPUT. How to do it?

10 November 2013 9,638 5 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

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