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Questions related to Molecular Dynamics Simulation
I did a tensile test of a specimen of flexible epoxy matrix. Upto which point in the curve should I consider to determine the youngs modulus?
02 June 2024 1,519 3 View
I read An article of synthesis of Thiazolidine derivatives by reacting Schiff bases with thiaglycolic acid & heated them in a microwave oven for 10---15 minutes (425 watt) , no temperature...
28 April 2024 8,056 0 View
Hello everyone, in the gel results image provided, the samples in lanes 2 and 5 represent linearized plasmid DNA from groups A and B respectively. Additionally, the samples in lanes 3 and 6 depict...
26 April 2024 7,058 1 View
What other relevant criteria can be considered to decide the best docked structure, aside from the pose with the lowest docking energy (binding free energy), which is considered the best...
17 April 2024 3,064 0 View
In the journal, "THE TRANSITION FROM GEL SEPARATORY SERUM TUBES TO LITHIUM HEPARIN GEL TUBES IN THE CLINICAL LABORATORY" by Oğuzhan Zengi, how do the results of Bland-Altman plots and regression...
10 April 2024 7,195 1 View
I am designing some donor-acceptor-acceptor type compound . I am check their electron mobility and the nature of organic semiconductor either n-type or p-type. what type of organic semiconducting...
02 April 2024 1,470 0 View
The gromacs tool do_dssp (freeware) uses the dssp program for a graphical output. In it's -cs output (scount.xvg) it gives you the secondary structure in the following form: @ s0 legend...
29 March 2024 8,361 2 View
I grinded sunflower seeds to fine powder, did Soxhlet extraction using 95% methanol as a solvent overnight. To the resulting solution, i added hexane and water. Put in the separation funnel and...
25 March 2024 6,223 1 View
I have calculated the RMSD. I want to edit the trajectory such that all those frames that have an RMSD value greater than a threshold are saved in a separate trajectory. Can anyone help me with this?
21 March 2024 7,610 1 View
As per suggested i optimize molecule in semi emipirical Am1,pm3 set and reoptimize it in dft . And directly optimize from gaussian input file . But optimize geometrical parameter and mulliken...
10 March 2024 6,603 2 View
what would be the commands in the input file for Spin-orbit coupling constant calculation in ORCA?
07 March 2024 3,727 1 View
Greeting, currently working mixing of thermoset and thermoplastic polymer to from a coating. I would like to study in term of diffusion either both material miscible or immiscible between these...
08 February 2024 7,579 2 View
Dear Researchers, We are seeking to conduct a dilatometry test on a cylindrical green pellet of doped ceria ceramics featuring dimensions of Diameter = 8 mm and Height = 20 mm, encompassing a...
11 January 2024 1,815 1 View
I am using a pET28B vector to clone my 2.1kb insert digested with BamH1 (fwd) and Xho1 (rev) restriction enzymes. I'm using over 1ug of DNA for restriction digestion, kept at 37°C for over 3...
10 January 2024 923 4 View
Is there a way to analyze labile carbon and refractory carbon using an elementar analyzer?
09 January 2024 2,193 3 View
Dear community! I wish my message find you well. I need to simulate rolling wheel and I need to define a local coordinate system at its center to define rotation angle of the wheel about its axis....
08 January 2024 3,540 1 View
Greeting, in my study I am using reinforced polyester as primer with addition of self healing agent. What should be suitable testing/characterization in order to study the self healing as well the...
03 January 2024 1,704 8 View
Hello, I want to perform 100ns GROMACS simulation using CHARM27 force field on a protein-ligand complex where my protein is CYP51 (PDB ID: 5V5Z) which contains a heme group covalantly bonded to...
27 December 2023 9,219 2 View
If $f_0^0$ is the Fermi-Dirac distribution function, and if the first line of the attached Fig is correct, then is the second line correct? ∂_{a/b} are derivative over $k_x$ and $k_y$. If the...
27 December 2023 6,351 0 View
In Gromacs we have Pull code, is there any code or options related to pushing back the molecule or part of it after pulling it? I want to see if the conformation or any other structural events...
20 December 2023 7,484 2 View
how we Integer nanoparticles in paints?
15 December 2023 9,430 3 View
My team conducted a prospective objective clinical study where we followed-up cancer patients who took a certain medication while undergoing conventional chemotherapy. We used objective reponse...
15 December 2023 9,452 1 View
Hello, total beginner in genomics and bioinformatics. We have modified HEK293 in our lab and we sequenced its Whole Genome (Pacbio long reads, mapped on hg38). I would like to identify the...
14 December 2023 9,555 1 View
Do you know of any online resource to computationally screen a patch in a protein structure for drug-like ligands?
12 December 2023 8,257 1 View