How to calculate the acceleration/velocity of different molecules in an MD Simulation?

Hi, If I am performing an MD Simulation in which the two groups/molecules are moving in a direction on applying a force on the system, how would I calculate the velocities/acceleration of the two?...

08 February 2021 9,525 4 View

Why the difference between degrees of nonclassicality of the input states is required for nonzero entanglement in the output state of a beam splitter?

By considering two single-mode Gaussian states at the input of a beam splitter, it is seen that the entanglement of the output two-mode Gaussian state depends on the difference between the degrees...

22 January 2021 3,490 3 View

Model reduction using Machine Learning techniques (...see description) ?

If we have a SISO dynamical system, for reduced order approximation using ML algs, do we need to take (frequency/ time domain) samples of Impulse response/TF Then to approximate this input/output...

08 January 2021 7,720 3 View

Is there anyone who can help me parameterizing theligand molecule with AMOEBA polarizing force field for using it in AMBER?

I am able to generate the parameter topology files for protein and water box using TINKER but am not able to generate these for my ligand as it is finding no atom types and atom class in TINKER....

17 December 2020 4,309 1 View

Can anyone please help me using polarizable force fieild in Amber18?

I am using force field ff02 and water model POL3. I am having difficulty in minimizing the system. In the Minimization output file after 100 steps of minimization EPOLAR = ************ EEL =...

17 December 2020 334 3 View

Future of construction systems?

Do you think that the automatized 3D-printing technique will replace the traditional building method?

10 December 2020 2,052 12 View

Gate All Around vs Continuous FinFET Thermals?

Can anyone help me know/compare the thermal challenges and limitations that gate all around have over normal continuous Fin devices. I understand that current density are bound to increase but...

20 December 2019 9,687 5 View

Why it gets slight shifted in (FT-IR measurement) peak location and change the relative intensity of the PEGs peaks?

In FT-IR spectroscopy measurement for pure PEG8000 and PEG8000/1wt%GO nanocomposite films , why it gets slight shifted in peak location and change the relative intensity of the peaks?

07 February 2019 4,094 5 View

Under any temperature and pressure can be prepare a homogeneous solid solution from the Al-Ni-Cr alloy?

14 January 2019 7,623 9 View

Cyclic loading in ANSYS ?

How can the Cyclic and repeated loading be represented in the nonlinear finite element program(ANSYS software)?

31 December 2018 1,705 7 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

What thickness need for ITO to use as conductive layer?

I want to do RF sputtering of ITO on glass substrate using magnetron sputtering. what thickness do i need to make it good conductive layer to use it for PSC. Moreover, whats about thickness of...

01 March 2021 395 3 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View