Chi Pui Jeremy Wong

10 Questions 11 Answers 0 Followers

Questions related from Chi Pui Jeremy Wong

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

In PSI4, there is an option MOLDEN_WRITE(SCF), but the default is false. How can I change the default to be true?

10 October 2015 8,422 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...

06 June 2015 985 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.

10 October 2014 9,192 1 View

In GROMACS, is it possible to select the atoms according to their Cartesian coordinates?

I would like to select the atoms according to their z coordinates. For instance, if I want to select all the atoms with the z coordinate values equal to or larger than 50 Angstroms (I do not care...

09 September 2014 314 3 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...

09 September 2014 1,964 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...

08 August 2014 1,226 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...

08 August 2014 4,451 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...

07 July 2014 6,155 5 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...

07 July 2014 5,055 1 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.

07 July 2014 8,287 1 View