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Questions related to Molecular Dynamics
Why the F and H atoms on the same side of the vinylidenefluoride groups but called trans structure?
23 April 2023 8,285 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 7,603 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 3,402 3 View
Reaction conditions : 60degC under inert atmosphere, and drying at 60degC. ZnO phases were observed in SAXS after drying.
22 March 2023 6,059 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 8,965 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 4,136 2 View
Various dope ions, for example; Is there an article that examines the capacitive behavior of electrodes doped with oxalate and sulfate ions ? To put it more clearly, for example, if I add...
14 November 2022 6,165 0 View
1.Whether to add quantum well model in the simulation? 2.After I added the piezoelectric polarization model, there is no polarization charge. What is the reason? 3.When I apply a large negative...
08 November 2022 596 0 View
Please give answer with proper explanation. ICP-AES is one of the method I know but I want another sophisticated, less sample required and easily available instrumental technique which can derive...
01 November 2022 3,649 0 View
I have a the absorption spectrum + the emission spectrum. I need to calculate the JO parameters for Tm3+ doped phosphors
31 October 2022 6,586 0 View
I'm studying heavy metal toxicity in wheat. I need to prepare a standard for GSH measurement, and I could not determine the appropriate GSH standards. Does anyone have any information?
16 October 2022 4,846 3 View
I am using a Windows 10 computer and have installed VMD 1.9.4a53 since it is 64-bit and allows for larger simulation files to be loaded without crashing. However, is it faster to use bigdcd when...
12 October 2022 6,654 0 View
I found that hydrophobic comprised of many types such as pi-sigma interaction, alkyl interaction etc. What are the differences between them? Can someone enlighten me? I am still new in this field....
27 September 2022 5,647 1 View
additionally, how can we calculate different cooling rates when we melt a system up to 3300k and quench at room temperature for 10000000 steps
06 September 2022 1,397 7 View
I am looking for ideas to quickly and cost-effectively confirm in the lab how well different types of plastic-wax mixes disolve in bitumen in order to have an idea of how my molecular models are...
10 August 2022 2,151 0 View
Any specific reason for the unfavorable Bump. What is an Unfavorable Bump?
24 July 2022 1,129 0 View
Residues in α-helices typically adopt backbone (φ，ψ).How can I get the number of residues localized within (φ，ψ) in a gromacs simulation?
09 July 2022 1,440 0 View
Hi everybody Previously, I have worked with BIOVIA Discovery Studio on windows operating system and now, I am working with ubuntu. I need BIOVIA Discovery Studio for linux and its installation...
29 June 2022 538 6 View
Colleagues, I need suggestions for PDB complexes with ligands (organic molecules) that prove difficult to validate by redocking, regardless of the program. Suggestions in the comments, and thanks...
04 June 2022 4,206 0 View
Hello, Normally, the lattice constant increases with addition of rare earth doping which is owing to the difference in ionic radii of rare earth ion and Ti4+ ions. However, in my present case,...
18 May 2022 6,150 1 View
I am using PyRx as platform when I load macromolecule and ligand, the molecules get loaded. When I Dock I get this message " >>Python 2.6.5 (r265:79096, Mar 19 2010, 21:48:26)" Can anyone...
03 May 2022 5,766 4 View
I have some apoptotic proteins identified from breast cancer datasets. I have a general queres in my mind. 1) How does apoptotic proteins function in cancer cells? 2) Would inhibiting an...
22 March 2022 228 4 View
Hello, I have ran MD simulation using NAMD and CHARMM36 forcefield and want to calculate RMSD values of multiple residues.(EX: RESID1 to52,133-193,281 to 296)How can I calculate this using VMD? I...
18 March 2022 5,742 4 View
Dear researchers Would you please guide me about the temperature of quantum espresso calculations? For example, relax analysis or phonon analysis is in 0 Kelvin or room temperature? Thanks
05 March 2022 130 4 View