Hi there,
I want to know how can i determine fluctuations, flexibility, and stability of a certain stretches of amino acids (for example amino acids 20 to 50) within a protein after MDS with GROMACS?
Regars
Thanks Stephane
If someone uses a cut-off ELISA kit, is it possible to use the ODs for comparison of sample data to control groups and not only report positive and negative?
09 October 2018 7,588 4 View
Hi, Recently, I performed a MDS with Gromacs and did not neutralized the system. MD was ran and nothing happened. I wonder what will happen in a non-neutral MDS. Can it be used for analysis? Regards
08 September 2018 6,455 4 View
Hi there, I need to import a DNA molecule into a crystallographic pdb file containing a viral capsid. Furthermore, I want to add some ion molecule surrounding the viral structure. Is there any...
07 August 2018 8,524 5 View
Hi, I have a single-stranded circular DNA with ~6k genome size. I want to choose a good DNA Seq platform. Can anyone help me with that please? Regards, Alireza
06 July 2018 8,184 2 View
Hi there, I have a stock solution of a clinical isolated phage with a titre of ~3E12 pfu/ml. Is it high enough for TEM microscopy, and is there any other considerations for imaging? Regards Alireza
05 June 2018 1,089 2 View
Hi, I have extended my MDS using Gromax according to this: gmx convert-tpr -s md_1.tpr -extend 9400 -o md_2.tpr gmx mdrun -s md_2.tpr -cpi md_1.cpt -nb gpu -v However after simulation done, I...
04 May 2018 2,736 5 View
Hi there, I have a forest plot of a meta-analysis. From 13 studies with same method and same subjects I have 2 studies in same country, which are outliers. The studies have two different sample...
03 April 2018 531 9 View
Hi, I have extended a simulation from 10ns to 100ns with following command: gmx convert-tpr -s md_10ns.tpr -extend 90000 -o md_100ns.tpr and: gmx mdrun -s md_100ns.tpr -cpi md_10ns.cpt -nb gpu...
02 March 2018 480 1 View
Hi there, I have found a paper presenting results in which human cytomegalovirus load has been assessed in biopsy samples. The paper did not mentioned whether the samples were paraffin-fixed or...
01 February 2018 4,052 3 View
Hi, I have used a magnetic-based DNA extraction kit. At the final step, when I want to dissolve DNA from magnets in elution buffer (Triss-EDTA pH=8.5), the magnet dyes are dispersed into the...
31 December 2017 9,686 4 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
03 March 2021 9,989 2 View
I'm involved in a study of odor control technologies for municipal wastewater treatment plant. One of the control options involves a chemical 2-stage (acid/alkaline) packed bed scrubber. The...
03 March 2021 3,661 2 View
I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...
02 March 2021 4,443 2 View
Hi all, I need to cleave the ester in Ethyl 2-amino-1H-imidazole-5-carboxylate to make the carboxylic acid and retrieve the product from solution to use in downstream applications of linking to...
01 March 2021 8,766 3 View
I am doing a acid and a chiral amino alcohol reaction using DCC and HOBT in DCM or THF? Can anyone suggest me how to remove DCU and HOBT from a reaction mixture??
28 February 2021 2,153 1 View
Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...
28 February 2021 5,650 1 View
hi everyone, I'm interested in the field of vaccine design specifically multi-epitope cancer vaccines , I want to know if there is a minimum and maximum number of epitopes we could use in a...
27 February 2021 3,882 3 View
Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...
26 February 2021 10,014 3 View
I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...
25 February 2021 6,314 1 View
I am working with Polyacrylic acid (100.000Da) and instead of water, I need to use another solvent (dioxane) to dissolve PAA. However, because of the high molecular weight, it's quite hard to...
25 February 2021 2,225 5 View