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Questions related to Molecular Dynamics Simulation
Hello I am trying to optimize the methane structure to find the Free Energy and apparently there is something wrong. I included my input file as well as a log file and would like to know how to...
18 September 2025 5,423 1 View
i'm trying to do the protein and ligand (cyclic pepide) docking using pyrx. after loading i'm not able to do forward in pyrx window. is any other way to do it or any other software for do the...
21 May 2025 9,556 2 View
I want to make a 3d qsar model for a series of compounds. I am planning to do an MIF based QSAR, preferably using CoMFA. Please suggest a free and open source tools for this.
01 May 2025 473 0 View
i run a relaxation calculation in quantum espresso and convergence had been achieved, but i couldn't see final coordinates.
13 April 2025 464 4 View
What will be my sample size? What would be my research tools? What will be my literature review? What will be my statement of the problem? What will be my research methodology?
08 April 2025 2,105 1 View
I'm trying to perform a docking experiment using the GOLD software. To do so, I initially prepared my ligand in CHIMERA, added hydrogens and charges (protonation state +3). However, after running...
19 February 2025 536 1 View
I have been trying to perform docking with autodock4 and it seems like the operation starts but never completes. The attached dlg file doesn't show any results and I am not getting any error...
14 February 2025 5,251 2 View
PBEPBE functional optimization keywords in Gaussian 09?
02 February 2025 2,967 2 View
PBET is a user-friendly computational tool designed to estimate the potential biological activity of phytocomplexes (mixtures of plant-derived compounds). It achieves this by: Molecular...
01 January 2025 4,626 0 View
I have predicted (human) resistin structure using modeller, phyre and itasser and none of the structures I received showed suitable binding energy with known drug (eg-masoprocol) after docking,...
09 November 2024 2,765 4 View
I want to know more about ophiolite melange ages.
15 October 2024 2,368 0 View
When using an RNA extraction kit, we consistently encounter the issue of genomic DNA residuals. Despite using DNase treatment, we never seem to fully eliminate the contamination, which suggests it...
16 September 2024 8,146 3 View
I want to know more about orthopyroxenes.
13 September 2024 3,378 3 View
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28 August 2024 6,595 0 View
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 1,809 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 8,253 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 7,324 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 3,290 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 7,421 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 1,673 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 8,616 2 View
Experiments were conducted in the order 2-cyclohexen-1-one, cyclohexanone and mixture. The peak of cyclohexanone appears as one peak. Why does 2-cyclohexen-1-one have two large peaks and two...
29 March 2024 4,919 0 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 6,454 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 7,843 1 View