How can the MOLDEN_WRITE(SCF) be switched on in PSI4?

09 October 2015 8,411 1 View

Is there any difference between using Gaussian distribution and pseudo Voigt profile in the curve fitting of XPS data?

Recently, I have written a Python program, which can fit the XPS data to a Gaussian distribution. The sample I used in XPS experiment is PMMA. The data were fit well to the Gaussian distribution...

05 June 2015 964 3 View

What command do I use when I want to calculate the surface tension on GROMACS?

I have a system with two interfaces, and I would like to calculate the surface tension.

09 October 2014 9,175 1 View

Is the characteristic ratio of a polymer dependent on its density?

It is well known that the characteristic ratio can be used for the analytic calculation of end-to-end distance and the gyration radius of a polymer with a Gaussian coil structure. The...

08 September 2014 1,954 3 View

How should I edit the index file for the calculation of order parameter of polymer carbon backbone using g_order on GROMACS?

The gromacs manual says that the order parameter is calculated by inputting the angle between a vector and the z axis into an equation. So, if I would like to calculate the order parameter of the...

07 August 2014 1,217 12 View

Where can I find the literature values of the barrier energy between the trans and gauche conformations of all different types of polymer?

For example, the barrier height between the trans and gauche conformation of polyethylene is 10kJ/mol (about 2.5RT), which means that the C-C bond of the backbone can be rotated quite easily. I...

07 August 2014 4,441 1 View

How can I use the final structure of one simulation as the initial structure for another simulation on GROMACS?

Say, I have performed a NVT simulation, and have got a trajectory file. After that, I would like to extract the final frame and change the dimension of the system, and use it for another NVT...

06 July 2014 6,140 5 View

How can I plot the energy as a function of torsion angle on GROMACS?

Which command do I need to use? To my knowledge, the g_angle and g_energy commands can only plots the torsional energy as a function of simulation time.

06 July 2014 8,274 1 View

Is there any work in the literature comparing the surface tension of spin-cast thin film of PMMA with different tacticities?

If I prepare thin films of atactic and isotactic PMMA by spin-coating method and measure contact angles of deionized water on these films under room condition, are the contact angles of these two...

06 July 2014 5,044 1 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

Do anyone here can help us in the field of molecular docking?

We have synthesized various metal complexes with different environment around the metals. Now to see the application of synthesized complexes we need this study also. we are also interested in...

01 March 2021 1,899 2 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

How to formulate Energy minimization in Molecular dynamics simulation for alloys using meam potential?

during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...

22 February 2021 380 5 View

Magnetismic Gravity in the universe?

MAGNETISMIC GRAVITY What is magnetism? Something magnetic has a + and - charge. If 2 + or - are pushed if + and - are pulled. But what is the main reason for this? Why does magnetism have a pull...

21 February 2021 9,538 3 View

Has anyone succeeded in capturing uranium atoms in a fullerene structure?

Additional questions are: What are the encapsulating atoms? How difficult was the process and what rates were achieved? What factors most seriously affect the economics?

20 February 2021 3,134 5 View