I just want to know if there is any gromacs command or I have to write a code
https://www.researchgate.net/post/How_to_calculate_rotational_diffusion_in_gromacs
please check gmx rotacf
I am working on Abaqus/Explicit(Quasistatic ) for the deformation of the auxetic structure model. Please explain how the plastic input value should be considered from the true stress-strain curve...
05 August 2024 453 3 View
How to enhanced h-index in Research Gate?
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I want to do wavelet transform of some compounds for their comparative study? Kindly help me in this regard and provide with proper procedure.
31 July 2024 4,170 0 View
I am using CuBr/THPTA for a click reaction in total cell lysates. I am facing issues with my protein sample in non-reducing SDS-PAGE where it's not migrating properly and most of it remains at the...
29 July 2024 949 4 View
How to use energy flexibility in inventory modeling?
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Please send me updates regarding the above-mentioned areas in the question mark?
28 July 2024 5,197 3 View
The resin bonded carbon containing refractories are aged before use. How time of aging is determined? And mechanism behind aging.
23 July 2024 3,205 0 View
I'm facing issues with the tumor dissociation protocol for GBM. I use collagenase/dispase with DNase to dissociate my tumor sample. However, even after incubating it for 60mins, I do not get a...
22 July 2024 412 3 View
In breeding trials, environmental variability can significantly affect the results, making it challenging to accurately evaluate the performance of different lines and hybrids.
22 July 2024 3,961 4 View
I have read papers where markup has been taken to measure market power. However, if markup data is unavailable, is it okay to continue with profit margin, as when a company has market power, it...
22 July 2024 706 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
Why is the molecule's orientation with an electric field affect polarizability? Electrons are diffuse enough to be independent with respect to orientation and effect of electric field on...
03 August 2024 7,843 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 366 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 4,588 1 View