Is there any molecular dynamic simulation study done on cell wall of bacteria?

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Can anyone help me with my problems pulling a molecule across the lipid bilayer in a steered MD simulation in GROMACS?

I am using following pull code in the steered md simulation in gromacs for pulling a molecule across the plasma membrane model. ; Pull codepull = umbrellapull_geometry = distancepull_dim = N N...

03 April 2015 282 6 View

Pressure and density values not converging to reference values in membrane simulation in gromacs 5.0.4 ?

I am trying to simulate the membrane patch of 5 lipid mixture obtained from the CHARMM-GUI (I edited the output README file as 1 to 20 for getting a total of 20 ns production run, and all...

02 March 2015 8,702 3 View

GRID computing, how to setup a grid computing over the local area network, in case of molecular dynamic software (is it possible with gromacs or NAMD?

GRID computing, how to setup a grid computing over the local area network (LAN). In case of molecular dynamic software, is it possible with gromacs or NAMD to use grid computing to increase the...

01 February 2015 6,330 3 View

In CHARMM-GUI online server .mdp output file for equilibrium and production run has no pbc condition defined?

In CHARMM-GUI online server .mdp output file for equilibrium and production run has no pbc condition defined by default. So here I have to add pbc condition manually to all .mdp file, or no need...

01 February 2015 5,200 3 View

On which basis I should choose the lipid type for PC, PE etc, if I need to model the human Macrophage membrane?

On which basis I will choose the lipid type for PC, PE etc, if I need to model the human Macrophage membrane among (because chain length of fatty acid and fluidity of the membrane will vary with...

01 February 2015 3,901 1 View

Fatal error: Group pull_group1 required by grompp was undefined?

I followed tutorial exactly same as mentioned on http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html for umbrella sampling but following command produced...

01 February 2015 4,523 4 View

How do I solve this error and how I can install gromacs through yum?

Getting error during gromacs 5.0.4 installation on centOS 6.6 -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2Downloading:...

31 December 2014 349 9 View

Can anyone suggest me how to do/check the effect of variable ph range (acid expansion) on the protein structure by Gromacs MD simulation?

As we know that there is acid expansion of protein when we change the native ph of the protein. I want to prepare a protein at ph 4.7 (protonation state, as assay system was set to 4.7 ph) which...

10 November 2014 4,134 7 View

Do you think that MTH1 inhibitors can be a break-through in cancer treatment without any, minimal or acceptable side-effects?

10 November 2014 2,476 4 View

Which Scopus Journal provides the most affordable fees?

"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....

10 August 2024 8,621 1 View

Seeking Advice on Viability and Execution of Undergraduate Thesis Topic?

Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...

10 August 2024 8,992 0 View

Why Do TDS and EC Increase with Larger Wastewater Volumes, While BOD and COD Decrease?

I have carried out MFC experiments on three different volumes, 50, 500 and 1000 mL of wastewater. Results after MFC treatment shows that TDS and EC are more in larger volumes of water i.e. TDS and...

09 August 2024 9,621 0 View

Could it be a cell culture contamination?

Hello everyone! I observed in my culture (htert-RPE1 cells) an orange- red particle at the bottom of the dish. It is visible to the naked eye as a very very small red dot. Could it be a...

09 August 2024 2,824 3 View

Who will be moral responsible for the death of thousands of people in the event of an earthquake?

Who will bear moral responsibility for the deaths of thousands of people in the event of an earthquake? Weeks and months remain before the onset of strong earthquakes that bring death to...

08 August 2024 6,134 12 View

Is there any way to quantify bacterial and fungal cells in their mixed culture?

I am working in fungal fermentation of soybean meal and there is bacterial growth in them at times. I am trying to quantify fungal cell counts and bacterial cells; but I haven't been able to do at...

07 August 2024 7,535 4 View

What precautions should be taken while handling S. aureus enterotoxin Type B in the lab?

I would like to understand potential safety concerns while handling SEB in the lab. Especially while working in animal house facility. Would like to know precautions for handling. Sigma MSDS...

07 August 2024 6,034 3 View

Why do i have a weak plasma and no coating during rf sputtering?

I have been getting a low plasma and no coating while doing rf sputtering of copper doped ZnS using a power of 140 watts and at pressure of 6.5x10-3 Mb.

07 August 2024 4,526 4 View

How to normalize and take the significance of the MTT OD values with 3 replicates for the same cell-line?

Hi, I have a question about normalizing the MTT OD values for doing the statistical analysis. So, if we have 3 different plates and we call them 3 different replicates, so, first we would...

07 August 2024 8,106 4 View

Why activated CAR-Jurkat cell could not kill targets?

Previously when I co-coluture anti-CD19(FMC63) CAR-Jurkat with Raji with E:T=5:1, Jurkat can eliminate Raji in 24h. However, when I test another CAR construct, although I can dectect totally CD69...

06 August 2024 641 2 View

Mahender Singh

Thank you Bhavin Pethani

Karl N Kirschner

hello Mahender,

My colleagues and I have published one on gram-negative bacteria, which should contains some additional references for you to follow:

http://pubs.acs.org/doi/abs/10.1021/ct300534j

A quick search also shows:

1. Roberta P. Dias, Gabriel C. A. da Hora, Madeleine Ramstedt, and Thereza A. Soares Journal of Chemical Theory and Computation 2014, 10 (6), 2488-2497

2. Emilia L. Wu, Olof Engström, Sunhwan Jo, Danielle Stuhlsatz, Min Sun Yeom, Jeffery B. Klauda, Göran WidmalmWonpil Im Biophysical Journal 2013, 105, 1444-1455

Best regards,

Karl

thank you Dr. Karl N Kirschner