During calculation of RMSD distribution using "g_cluster", the Y axis of the XVG file denotes a.u. i.e arbitrary unit which I think probably the frequency. But it is not clear which frequency it exactly is as well as how the calculation happened.
Do you get RMSD distribution from g_rms?
My question is especially concerned with the bridge transition zone portion where the train at certain speed crosses the bridge main section to enter into the end transition zone. Is there any...
07 August 2023 1,947 4 View
I am working on an aromatic system of five membered heteroatom compound like methyl pyrrole. When I was calculating single point energy of Transition states for both additions by Cl-atom and...
23 July 2023 4,563 0 View
I learned from somewhere that ORCA is the most popular free and open-source computational quantum chemistry software developed by Frank Neese and others. Now, being a language enthusiast, I want...
01 June 2022 5,147 2 View
Any research article showing charge transfer through DFT would be highly appreciated
10 May 2022 6,036 0 View
I am performing fibronectin staining on Xenopus embryonic tissue. The tissue is fixed overnight in 4%PFA, permeabilized in 1xPBS with 0.3%TritonX, Blocked in 10%Blocking in 1XPBS with 0.3%TritonX,...
18 May 2021 3,386 1 View
Hello, I'm working with Arraystar lncRNA microarray for the first time. I tried to normalize the raw files (.txt) using the following script, which I used to normalize different other Agilent chip...
27 March 2021 2,622 1 View
I am trying to build the model of a protein using homology modeling. The available structures of the protein are partial. Specifically, the available structures are of specific domains/segments of...
15 October 2020 5,501 13 View
Its a book related to biostatistics.
27 April 2020 6,508 2 View
I am doing a project on super capacitor. there is no equipment or technology to capture the electrical energy in a strike or in a fraction of second. but if we reduce the resistance of the battery...
20 March 2020 1,717 1 View
I am trying to extrapolate damage in cyclic fatigue tests ( and if possible creep-fatigue tests as well). Without damage I have used the method by Bogard et al....
11 February 2020 9,864 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
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
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
In the peptide-HLA-TCR docking process, can we express the result of peptide-HLA docking in RMSD and for peptide-HLA to TCR docking, can results be expressed in binding affinity?
11 July 2024 4,831 0 View