How to restart simulation in Gromacs?

I tried to run a 500ns MD simulation of a protein in Gromacs. Due to power failure, my pc turned of after around 450+ ns. Now I want to restart the simulation from that point. I used the following...

13 November 2020 8,691 3 View

How to calculate RMSF per residue name vs time in Gromacs?

I have done 100ns simulation using Gromacs. To calculate the RMSF, I used the following command- gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res But when I plotted the graph in excel, I found...

12 November 2020 4,663 2 View

How can we make remote teaching and learning more interesting and engaging?

We ( Higher Education) started with Zoom, then Google Meet, and this term we will be using more updated and smarter system MS TEAM to make online teaching more participatory and engaging and...

12 August 2020 9,154 42 View

Is it possible solid state proton nmr with negative values?

I have done solid-state proton NMR. General solid-state proton NMR shows broad peaks. But, I find a negative value peak. In the case of solid-state, there should not use any reference (as...

13 July 2020 6,123 1 View

What is the convenient way to to measure the degree of cooperativity in DNA-DNA or DNA-protein interaction?

Hill equation is used to determine the degree of cooperative behavior in ligand -enzyme interactions. If I would like to utilize this equation in DNA-DNA or protein-DNA interaction, is it...

18 December 2019 5,712 2 View

If I want to run an abaqus job (in Linux redhat) with user subroutine on parallel processors, how do I do that?

Hello: I work in Abaqus 2017 a lot. I have noticed that when I submit any abaqus job (that does not contain any subroutine!) via parallel processing (aka cpus=4 or 8), it runs just fine! But,...

24 April 2018 5,516 2 View

What is the unit of the output variable (gap flow volume rate) in Abaqus Standard?

Hello: I am modelling for 2D hydraulic fracturing in Abaqus Standard, and adding proppant transport simulation to the this as well. I have three steps to my model. Geostatic Step2 (where I...

18 April 2018 6,844 4 View

Any way to read from a text file while running an abaqus job so that the abaqus job does not freeze?

Hello: I am trying to do a very simple thing that I just can't seem to do in Abaqus! I know how to create a new text file and write to it any output variables with any desired format I want!...

04 March 2018 6,249 2 View

RE: (Fortran Computing) Can anyone please tell me a fix to this problem?

Hello: I am very very new to Fortran programming! I am trying to practice coding in Fortran language. I am using Plato IDE (FTN95). I have written a code for calculating factorial of a number. The...

04 June 2017 1,929 9 View

What could be the reasons of the initial dip/peaks at the beginning of the melt curve?

A new primer pairs were designed for detection of Vibrio cholerae specific 'ompW' gene using real-time PCR machine ABI Step One. The expected size of the PCR product was 191 bp. Upon PCR...

29 May 2016 7,307 2 View

How to remove the residual PDMS on the silicon mold?

Incompletely cross-linked pdms are difficult to remove.

01 March 2021 798 3 View

1 nm thick MgO thin-film to be deposited on Si wafer using thermal evaporation. What will be the optimum deposition conditions?

Favourable conditions of base pressure, rate of deposition. Also, by which characterisation technique to be used to verify the thickness of the deposited film.

28 February 2021 3,640 3 View

How to use measure capacitance change in COMSOL time dependent study ?

I want to measure change of capacitance due to relative displacement between two parallel plates in COMSOL. Distance between two plates changes with time. So I'm using a time dependent study but...

26 February 2021 8,567 3 View

How to calculate Z (the number of molecules in a unit cell) for calculating theoretical density?

I am trying to calculate the theoretical density of my ceramics materials. I use the formula below to calculate the theoretical density: Theoretical density = (Molecular weight x No. of molecules...

24 February 2021 3,823 2 View

How to prepare a thin polymer film by post-polymerization/crosslinking?

24 February 2021 2,362 5 View

Is is possible to pole with corona poling pellets of the sample material instead of thin films?

As it is highly probable that pellets will have a higher degree of air gaps and voids than thin films, is it possible to pole the samples with corona poling nevertheless? Or is there the...

24 February 2021 1,349 1 View

How to troubleshoot Electrochromic Films and Electrochromic Devices?

I am trying to characterize an electrochromic system. The system uses ITO electrodes on glass, WO3 as the electrochromic film, and NiO as the ion storage layer. When I deposit NiO and WO3 and...

23 February 2021 9,592 2 View

Can't recognize exact phase and PDF card no of Silicon carbide in XRD?

We have deposited silicon carbide on carbon substrate using one PVD technique. Due to amorphous behavior of SiC at low deposition temperature, we performed heat treatment of those films at...

22 February 2021 2,072 3 View

How to improve the adhesion between germanium and silicon monoxide thin film layers using EBEAM evaporation?

I want to deposit multilayer coating of germanium and silicon monoxide on silicon wafer using ebeam evaporation?

21 February 2021 2,141 3 View

How can I measure the thickness of thin layers deposited on textured glass susbtrates?

I want to measure the thickness of aluminum oxide and titanium oxide layers deposited on textured glass substates. The layer thicknesses are typically below 100nm.

21 February 2021 5,465 4 View