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

What is the difference between spark plasma sintering and electric resistance sintering?

It is well known that plasma sintering is based on the electrical spark discharge phenomenon for preparing high-density composites at lower temperatures and higher sintering speed. How it differs...

03 March 2020 4,458 4 View

Can anyone please help me with ECV ( electrochemical capacitance voltage) profiling measurement?

I need to measure carrier concentration profile in phosphorus doped poly-crystalline silicon thin film. Is there any group who has the facility to perform ECV ( electrochemical capacitance...

29 February 2020 8,270 2 View

Management and social science research question?

In management and social science research, what is the difference between the following- 1. A has a positive effect on B 2. A positively influences B 3. A has a positive impact on B

13 October 2017 4,332 3 View

What are the most important flavor compounds in Coffee?

I have read numerous papers regarding the chemical compounds that are most important for coffee flavor but all mention different chemical compounds with very little overlap. Obviously different...

12 September 2017 6,120 5 View

CopGFP Control Plasmid amplification

14 July 2017 3,934 1 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 long do NCI-H1299 cells normally take in order to adhere to a plastic cell culture surface following thawing?

How long do NCI-H1299 cells normally take to adhere to a plastic cell culture surface following thawing? and how can we improve the speed of adherence? We received the cell line from the ATCC. We...

05 April 2016 1,417 3 View

Can someone suggest a way to prepare slides to observe under confocal microscope for observing fluorescent tagged proteins??

I am growing the cells on coverslips and transfecting the fluorescent tagged protein directly on them. Then i want to observe these cells under confocal microscope. Currently i am just using...

01 March 2021 6,142 3 View

Will a 10xHis-tag prevent anti-MBP from binding to MBP?

I have a protein with a 10xHis-MBP tag on the N-terminus. I'm fairly certain I am expressing my protein, but I'm not getting a signal on my western blot. Is there a possibility that the 10xHis tag...

25 February 2021 8,404 3 View

How to minimise the risk of being abused the profile of potential participants tagged in a social media post?

Dear colleagues, I got this one in one project I did ethics review. It's great to hear about your thoughts/experiences. "Doing an open recruitment online (i.e., via Facebook) requires public...

22 February 2021 3,322 3 View

How to get the vector of a specific vibration mode in phonon dispersion?

For example, I have this phonon dispersion(Fig. 1), and now I would like get vector of atoms which describes TA1 in P. I know v_sim can show vibrational animation of specific mode, but I do not...

20 February 2021 4,332 4 View

Unable to detect a truncated protein variant, but I can observe a truncated cDNA from Sanger?

Hi, so basically... I am trying to mimic a clinically observed condition wherein a frame-shift mutation happens only at one allele of the patients, giving rise to a truncated variant which evades...

17 February 2021 1,130 6 View

Choice of Ab for Co-IP: Does an anti-(tag) antibody (such as anti-flag/ anti-myc) a must if I am using co-transfected cells for Co-IP?

Hi guys, I am trying to detect the binding of 2 proteins by Co-immunoprecipitation. However, the choice of antibody is confusing me. I tried probing the endogenous protein right away but the...

16 February 2021 9,050 5 View

Can anyone suggest me broad host range fluorescence expression vectors for Gram-positive bacteria ?

Hi everyone, I am looking for fluorescence expression vectors for expression in gram-positive bacteria present in the skin microbiome. I need to tag them with a fluorescence marker and observe...

06 February 2021 2,566 4 View

Can anyone suggest a numerical method to calculate perimeter of a contour in charge density contour maps?

Hi i have drawn the charge density contour maps using VESTA taking CHGCAR files from VASP. Now, What I Want is that I need to know the perimeter of each contour appearing in the cross section 2D...

04 February 2021 3,637 1 View

FLAG purification, elution doesn't have protein?

I am purifying a heterotetramer, with one subunit having a 1D4 tag and the other having a FLAG tag. I purified from Sf9 with HBS pH7.3 and 0.002%LMNG first with Anti-1D4 resin and got an adequate...

02 February 2021 3,860 1 View

Antibody dilution for IHQ in OCT frozen tissue is more similar to IHC in Paraffin-embedded samples or to Immunocytochemistry?

31 January 2021 8,678 3 View