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Questions related to Molecular Dynamics
When the third-order absorption coefficient is negative, it indicates a reverse saturable absorption (RSA) behavior. In materials exhibiting reverse saturable absorption, the absorption decreases...
11 November 2023 8,408 0 View
I was trying to prepare the ligand-binding domain of human estrogen receptor beta (1QKM: https://www.rcsb.org/structure/1QKM ) for docking and met the following error on the stage of .pdbqt file...
30 October 2023 1,436 0 View
Special&general relativity, one the pillars and one of the 3 more successful physical theories, gives a prime or hierarchically high role to the properties of light, which are the...
25 October 2023 4,130 3 View
Hello every body I want to do umbrella sampling following Mr. Justin Lemkul Tutorial. I simulated and prepared lipid bilayer by version 4 of gromacs before, now in continuous in order to do the...
23 October 2023 7,925 3 View
The so-called "tunelling effect" gives a non zero probabilitu for an electron to surpass a potential barrier i.e violates the fladsic "energy battle rule"(between energy and external potentials)...
19 October 2023 1,340 2 View
when I use autodock ,I have this problem : C:/Users/cppyq/autodock4.exe: FATAL ERROR: C:/Users/cppyq/autodock4.exe: I'm sorry; I can't find or open...
28 September 2023 4,165 1 View
I read on the G09 website that ADMP is equivalent to BOMD (Born-Oppenheimer MD) simulation. But it is unclear to me, how to perform it. Is there ant keyword? Can we do it using GaussView?
02 September 2023 459 3 View
I am writing to seek assistance on a matter related to n2t file generation. I am using GROMACS and charmm36 force field in my work. I am covalently attaching a short polymer(poly-peptide) to a...
31 August 2023 8,184 2 View
Does dissolving salt change water volume and how does the amount of salt dissolved in water affect its density?
31 August 2023 8,503 3 View
Hello. I first treated glass substrates with piranha, coated them with gold, then attempted to do a surface modification with MUA dissolved in DMF. Once adding the DMF solution, the gold layer got...
25 August 2023 7,539 6 View
Hello, I am working on heavily doped TCOs for solar cells integration. I am currently trying to draw band diagrams, but I am facing a problem. I am able to characterize the work function (WF) of...
17 July 2023 5,313 8 View
Say we have an XRD pattern that shows peaks for both (111) and (222) planes. Does it mean the crystal has a property that a similiar material that shows only the (111) peak doesn't have? Thanks...
07 July 2023 3,511 1 View
I want to generate a trajectory using my MD data that only contains solvent and solutes that are smaller than the 0.35 limit. I make the index file of those residue. From one frame to the next,...
06 July 2023 4,529 2 View
I have a protein. It's binding site are not known hence I used castp for the prediction. I set the grid box in autodock vina and performed the docking with a ligand. However, when I see the...
05 July 2023 3,486 3 View
if there is an amber command line for that, how will it look like because the one i used made both peptides overlap
27 June 2023 3,401 5 View
Why is change in entropy lower for higher temperatures and difference between increase and decrease of entropy?
03 June 2023 2,880 1 View
Why heat added to a system at lower temperature causes greater randomness than when the same quantity of heat is added to it at higher temperature?
03 June 2023 9,512 1 View
We did a virtual screening of database using autodock vina. We started ranking the molecules based on docking score and observed three molecules of different chemical structure with same docking...
16 May 2023 7,578 4 View
Why the F and H atoms on the same side of the vinylidenefluoride groups but called trans structure?
23 April 2023 8,388 0 View
I did a GSH measurement on the samples today in -80. I used the Ellman method. Reaction comparison: 0.1 ml sample, 2 ml Tris 8.4, 0.1 ml Ellmann reaction. i measured it at 412 nanometers, but my...
14 April 2023 7,790 2 View
Dears, Which sampling method and which Formula I have to use for calculation of my sample size on topic of "comparison of safety and efficacy of Thalidomide vs Hydroxyurea in Transfusion...
01 April 2023 3,584 3 View
Reaction conditions : 60degC under inert atmosphere, and drying at 60degC. ZnO phases were observed in SAXS after drying.
22 March 2023 6,149 0 View
I have a big trajectory file (.dcd) after performing molecular dynamics simulation using NAMD. The size of this trajectory is about 180 Gb. Since I wasn't able to load it in VMD (due to the lack...
24 December 2022 9,068 0 View
Hello all. I have a .gro file, from which I have to delete certain number of hydrogen atoms from specific residues. I tried doing it manually, but the atom numbers get mixed up and the file does...
16 November 2022 4,263 2 View