How I use the installed version of Gromacs 2018 from my home directory in CDAC-BRAF server?
Please help me out..
thanx Muniba Faiza
I recently came across an anatomy text by Carl Moller that was published in 1915 but it is in German or Dutch neither of which I can understand. I would like to know if there is an English...
10 August 2024 4,347 1 View
I am writing a paper as a part of my course. I am new in London and was wondering that what publications should look upto?
21 July 2024 3,538 1 View
I am working on carbonic anhydrase immobilization into MOFs. I am facing problems with low enzyme loading.. The other issue is that when using p-NPA activity test to detect the activity of the...
20 July 2024 1,440 3 View
Hi all, I am trying to use mixed effect model to analyze my data, which including a baseline measurement for my exposure (A), and repeated measurements for the outcome (B). I do have some...
17 July 2024 8,682 3 View
i need to know the required time
15 July 2024 4,796 2 View
e.g. moment one: square in its normal state moment two: square after cutting large trees and replacing them with dwarf trees.
12 July 2024 8,258 5 View
Anyone kindly tell the name of software that make this graph quickly and also tell how we add vertices or lines in this graph with equal distance to get next dimensions of this graph ( i mean how...
11 July 2024 4,499 2 View
I participated in 2 research projects in which I was responsible for part of data analysis and figures production. Also, I spent hours trying a new statistical approach -for me- to implement in...
10 July 2024 1,226 5 View
I am simulating 1 cell of PEM with an area of 50 cm². The mesh has an orthogonality of 0.2 for the channels and bipoar plates (polyhedra) and a quality of 1 for the active zones (hexagonal). The...
26 June 2024 2,358 0 View
I have 3 different specimens. Each specimen has a main peak of the targeted phase, however, all of them also have a secondary peak of associated with a secondary phase. Now just based on the...
26 June 2024 5,049 5 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
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
To help enchancing patients flow and service efficiency
18 July 2024 482 2 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 everyone, This soudns like a strange question, but I created five XTC files using five different versions of GROMACS some years ago. All other files are missing, and I want to repeat the...
16 July 2024 7,205 2 View
Dear Gromacs users, I would like to simulate a zeolite-water system. In different literature, it is suggested to consider a rigid framework of zeolite to decrease the computational cost. I would...
15 July 2024 4,590 1 View