Are there any gromacs or other tools available to look for or find the number of protein-lipid contacts during Molecular Dynamics simulation of membrane protein ?
gmx mindist -on
You can also use Ligplot
This tutorial may be helpful for your analysis https://github.com/philipwfowler/simple-membrane-protein-analysis/blob/master/1-count-lipids.md
Hello, Can anyone provide me with the absorption coefficient of methane gas at 7.7 um? Any reference?
06 August 2024 980 5 View
Hello everyone! I am currently exploring the performance of large models in understanding knowledge in specific domains, and attempting to construct a knowledge framework similar to what...
05 August 2024 5,729 2 View
Regarding a model for simulating battery charge and discharge, what do you consider to be high fidelity? What is the acceptable percentage of error (regardless of the metric)? Could you suggest...
03 August 2024 5,358 0 View
need to open an account to upload my published papers
01 August 2024 9,255 1 View
All plants are green but some of these plants becomes yellow. I did not found any reason. Please help me to find out the real problem.
01 August 2024 589 4 View
I am using a Bruker 600M solid-state NMR spectrometer with a Micro 2.5 microimaging system. The test sample is a tube of 1M LiCl aqueous solution, and the nucleus detected is 1H. I am trying to...
01 August 2024 9,227 1 View
Hello. Thanks for your consideration to see my question. Recently, I conducted XPS anaylsis of g-CN that is prepared from thermal polycondensation of DCDA, so-called conventional bulk-g-CN,...
30 July 2024 9,824 2 View
N=6 Comparing pre and post test likert scale responses. Participants are mix of practicing & preservice teachers.
30 July 2024 7,233 4 View
Hello, I'm trying to measure the conductivity of semiconductor films but since I don't have a commercial four point probe set up I would like to build one on my own in my lab. I have generators,...
30 July 2024 906 2 View
Can an analytical method's limit of quantification (LOQ) be outside its linear dynamic range, or is it always required to be within it? Please provide a thorough explanation supported by verified...
29 July 2024 7,198 9 View
I'm working on selecting antibodies against a recombinant protein that has a His-tag. My idea is to first bind the recombinant protein to a HisTRAP column and then use this column for an affinity...
07 August 2024 505 3 View
I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
07 August 2024 2,598 1 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...
04 August 2024 1,200 2 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
Is it the "elution buffer" or the "dialysis buffer"? Note: I'll be using NanoDrop OneC
01 August 2024 967 3 View
Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...
31 July 2024 781 1 View