I am a beginner in the field of GROMACS.
I want to study the adsorption mechanism of citrate, oxalate, and pyrocatechol on hematite nanoparticles in the pH range of 9-5. Moreover, I want to study the presence of different electrolytes...
09 October 2018 7,329 3 View
I have created ZnO cluster in GaussView by increasing the lattice parameters in all three dimensions with total number of atoms as 32. Is it possible to know the size of this cluster from the...
02 March 2016 8,712 1 View
Is free version of CRYSTALMAKER software available for download? I downloaded demo version but that does not allow to save file.
03 April 2015 4,954 2 View
I am trying to simulate dppc lipid bilayer using OPLSAA forcefield. I downloaded 128-dppc.pdb, 128-dppc.top, dppc-opls.itp and opls-ua-lipid atomtypes.itp (contains only atom types) files from...
03 April 2015 5,984 5 View
I converted the pdb file to mol2file using openbabel 2.3.2. When I am trying to execute the topology of the file using the following command: ./topolbuild -dir...
03 April 2015 5,579 12 View
I created iron pyrite nanocluster in material studio 7.0 and exported it as .pdb file. I downloaded martinize.py to convert this nanocluster to coarse grain and create simultaneously cg.gro and...
02 March 2015 1,544 4 View
I want to build coarse grain model for metal oxide nanoparticles using GROMACS. CNT simulation steps are available on gromacs site (Andrea Minoia's tutorial) but I need steps for metal oxide...
02 March 2015 5,805 3 View
GROMACS
05 June 2014 2,117 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
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
