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Questions related to Molecular Dynamics
I have used g_mmpbsa (rashmi kumari version) for mmpbsa study in my previous simuation. Everything was ok. But i performed three simulations on cluster having gromacs 2021. Now the .xtc and .tpr...
21 May 2024 6,178 1 View
The inclusion of deformation energy and entropy corrections in MMPBSA binding free energy calculations is common in studies involving DNA-ligand complexes. However, in the literature, these terms...
26 April 2024 7,251 0 View
I have doped Er as activator and Yb as sensitizer in a borate host polycrystalline material
23 March 2024 3,817 3 View
While Newtons 2nd law cannot predict the constancy or upper limit of speed of light, c, its generalized version i.e.changing mass with constant acceleration definition can do. In other words,...
29 January 2024 9,425 4 View
Dear ResearchGate community, I have recently conducted two separate 100 ns molecular dynamics simulations using GROMACS, each involving a small molecule. My analysis of hydrogen bonding patterns...
18 November 2023 3,243 5 View
Good day, I created a grid using the Autodock tools and then using those coordinates and size I created a configuration file for Vina. But in the results, the location of the ligand do not match...
13 November 2023 2,797 2 View
It means that the number of electronic states per unit energy interval increases with the square root of the energy. There is continuous variation of energy which suggests bands have continuous...
11 November 2023 524 1 View
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 8,211 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 3,968 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 7,727 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 1,140 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 4,047 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 298 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 7,988 2 View
Does dissolving salt change water volume and how does the amount of salt dissolved in water affect its density?
31 August 2023 8,153 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 7,371 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 5,108 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 3,357 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 4,355 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 3,300 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 3,217 5 View
Why is change in entropy lower for higher temperatures and difference between increase and decrease of entropy?
03 June 2023 2,713 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 9,361 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 7,395 4 View