Need help in iTARQ data analysis?

Hello Everyone, I am doing iTRAQ (8plex reagent) experiment to identify and quantify the relative proteomic changes between control and test set of an organism. After labeling of different iTRAQ...

01 December 2019 4,554 3 View

Which heat transfer method is most efficient ? And how (mathematically) ?

for more clarity.

07 July 2019 985 9 View

How to check contamination while incubation of Mycobacterium tuberculosis (Mtb)?

21 April 2017 3,608 3 View

Are their any documents or standards available regarding the permissible limits of aloin concentration in aloe vera based food products?

I am searching literature on application of aloe vera for development of aloe based food products. There is very little information available regarding permissible limits of aloin content in aloe...

24 April 2014 3,208 1 View

COVID-19 Antibody- role in prevention

As some of the vaccine candidates have been given Emergency use Authorization (EUA), do we have the following clarity: 1. How many antibody values (titers) are protective? 2. What is average...

01 January 1970 8,613 1 View

How many number of years data are required for preparing a plan disease forecast model ?

Require for forecasting of yellow rust of wheat

01 January 1970 643 5 View

What element is driving the different slop in the low frequency tail?

My study consists simple corrosion inhibitors in salty brine. Right now I just fit my circuit with randles with CPE. Just wondering how the slop can given more info of the experiment. Or any...

01 March 2021 6,474 3 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View

Why does the sum of reaction forces not match the force component of a Free Body Cut in Abaqus?

I am using Abaqus to simulate a plate with in-plane loading. The boundary conditions allow the right edge to move up and down, the displacements on the left edge are fixed. There is no rotation...

23 February 2021 711 3 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

I want to simulate a system containing protein and heavy metals; which force field is most reliable for this purpose?

The protein I want to simulate has multiple heavy metals. I wanted to know which force-field I should use with GROMACS to achieve this. Most importantly, do the latest updates in the force-field...

16 February 2021 2,420 1 View

How to obtain parameters to run a simulation for benzene using CHARMM forcefield in GROMACS?

I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...

15 February 2021 5,561 3 View

Gromacs force field and water model recommended for protein hydrophobic study?

Dear All, I received a comment from reviewer about asking me selection of force field and water model. I choose OPLS-AAL and 3-point water model. They mentioned the combination of OPLS-AAL and SPC...

13 February 2021 1,364 3 View

Can anyone please suggest where I can find a reference for ReaxFF parameters for PTFE(Teflon) suitable for use in LAMMPS?

Trying to simulate a ice-PTFE interaction and am unable to find a reference which actually lists out forcefield parameters for PTFE-PTFE interactions using ReaxFF or even other force fields like...

08 February 2021 9,373 2 View

Anyone use GROMACS' pdb2gmx for Adenosine monophosphate (AMP) to use with CHARMM force field?

I am trying to use the following command in GROMACS to generate a CHARMM topology file: gmx pdb2gmx -ff charmm27 -f amp.pdb -o amp.gro -p amp.top The atom list in my pdb file (amp.pdb)...

01 February 2021 7,769 6 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

31 January 2021 6,321 1 View