How to calculate mixed membrane curvature with function of time in gromacs or other tools? can anybody help me to solve this problem?
Hello, I am looking for Gromacs utility that can be useful for the analysis two proteins or more proteins contact points in Martini coarse-grained simulations. Or any script file which can be...
03 April 2018 2,949 0 View
top of bilayer planer
02 March 2018 6,661 1 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
I am trying to coat my micelles and PLGA based nanoparticles with cell membrane using an Avanti mini extruder according to literature . I use 200nm membrane but my particles end up to be 400nm And...
30 July 2024 3,294 3 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
Does it exist some special technique for cutting ceramic membranes for Cross-sectional FESEM or SEM images?
25 July 2024 5,482 2 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
I have been using Gromacs 2021.7. I wanted to simulate two small molecules in water. But, while generating the ions.tpr, I am getting the following error. The topol.top and .itp files for each...
17 July 2024 9,897 4 View
i am using the trjconv command in gromacs gmx_mpi -debug trjconv -s md.gro -f md.xtc -o utr.xtc -fit rot+trans and after few steps i got the error gmx_mpi': corrupted size vs. prev_size:...
17 July 2024 6,216 1 View
Hello, I am currently working with Malaria Pf/Pan nitrocellulose membranes coated for malaria detection. After drying the coated membranes in an Incubator (overnight at 37°C), I've noticed that...
16 July 2024 7,937 1 View