How to use gromacs to build topology after peptide C-terminal amidation ？
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Hello everyone, I'm in the initial stages of conducting a study involving the ddPCR (Bio-Rad QX200, QX600) and I ran into some problems involving recovery % calculations using direct...
02 July 2024 6,011 2 View
I am trying the simulate the drum brake squeal in ansys. For giving the rotational velocity to drum what should i use the Rotational velocity or CMROTATE command.
24 June 2024 5,125 0 View
I need to get the eigenvalues after a modal analysis in ansys workbench. Is there any next APDL command that will get the required result.
20 June 2024 1,668 0 View
Can anyone recommend high-quality GSDMD antibodies for immunofluorescent or immunohistochemical staining in mice?
11 June 2024 6,948 1 View
I have an assembly of parts. I want to reduce the number of modes of the individual parts by CMS.
11 June 2024 2,966 0 View
I have two components for which I want to extract some number of modes shapes for each. Then using those model of the component I want to couple them together for non linear static analysis.
10 June 2024 1,234 0 View
I imported an 3D cad geometry in ansys. Now I want to create the mesh with solid45 element in workbench. How to proceed?
05 June 2024 2,490 1 View
I want to do modal analysis on a body which has two components which are in dynamic elastic and frictional contact with each other.
04 June 2024 8,493 6 View
Hi everybody! I got some strange results when I tested mitoSOX RED on Bone marrow-derived Macrophages. According to the publications, bone marrow-derived macrophages(BMDMs) generally show...
03 June 2024 9,853 1 View
Is the zirconium isotope of geological sample fractionated when passing through the column, and how to determine whether this fractionation is or not？
26 May 2024 6,721 2 View
We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...
08 August 2024 4,842 0 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, we have measured tryptic peptides using both DDA and DIA method on QExactive. In DDA replicates i saw unusual intensity drops occurring at the same sections of chromatograms in DDA replicates...
07 August 2024 3,218 4 View
Hello, I am currently analyzing some phosphoproteomics data, but I have peptides with multiple phosphorylation sites or phosphorylations together with carbamidomethylation or oxidation. How can I...
04 August 2024 8,432 3 View
Recently I'm trying to use Sep-pack C18 1 cc Vac Cartridge (Waters: SKU: WAT054955) to desalt digested peptides. However, the recovery rate is usually 40-60%. What is the normal recovery rate?
31 July 2024 6,544 11 View
Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar
29 July 2024 3,084 8 View
If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...
28 July 2024 673 3 View
Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...
24 July 2024 367 4 View
I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...
19 July 2024 4,120 5 View
So i have a few peptides (synthesized by SPPS and not cleaved from resin) and I want to add a maleimide label. We have NHS-PEG-Maleimide and from literature it is evident that the free amine group...
18 July 2024 4,075 3 View
