Dear All,
I would like to ask if anyone knows of any server that can give the gromacs 53A6 ff topology. I have to prepare my protein in that topology and use it. The ATB server is now only fixed at 54A7ff.
Any ideas?
I am new to research. The boiling point of triethyl amine (NEt3) is 89 degrees centigrade. I am skeptical that when I will let the hydrogen escape which is getting generated in situ, I will also...
21 July 2024 7,284 4 View
i want to delete my research paper.
09 July 2024 6,554 2 View
I'm working on the proteome (from Uniprot), as you're probably aware that there are reviewed and unreviewed proteins, however unreviewed proteins are in large quantities, but reviewed proteins are...
09 July 2024 5,782 2 View
Even adding fragrance is not working
05 July 2024 741 2 View
I have searched for CAS no. but cannot find.
24 June 2024 2,737 2 View
I am trying to run LDH assay on my samples using Hroiba ABX pentra 400. Multical has worked but negative and pos control are showing an error message saying no control in memory (image attached)....
18 June 2024 6,514 0 View
I have nearly completed my preparation for the short communication. However, I could use some assistance with the results. Any help would be greatly appreciated.
12 June 2024 4,230 1 View
I have tried combination of few monomers and resulting emulsion shows tack but tack is not enough to be measured by lap shear test machine, should I try new combinations or use some other method...
10 June 2024 5,305 3 View
How to calculate sample size for Quasi-Experimental Design Research?
21 May 2024 9,555 3 View
I have already prepared acrylic emulsion, but cannot find the way to add preservatives.
21 May 2024 7,248 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
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
Hello dear researchers, I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein. I have performed docking...
08 July 2024 4,724 4 View