While making movie of GROMACS trajectory in VMD, How one can stop motion of protein going from one direction to the other in PBC box?
I have a system with two proteins and a membrane as following protein-1, protein-2, and membrane bilayer. I would like to know whether the protein-2 binds first to protein-1 or the membrane to...
06 July 2018 10,093 1 View
I would like to validate a homology model. After peroforming MD simulation, one way is to check the stereochemical quality, Ramachandran plot, dssp, B-factor, etc and map the model with the...
06 July 2018 6,240 11 View
I would like to set the default background in vmd as gradient. Therefore I tried the following method to set default background gradient in ~/.vmdrc file but that did not work. Could anyone please...
05 June 2018 9,821 2 View
I have installed VMD 1.9.2 on Ubuntu machine and when I try to change the representation from lines to cartoon the GUI becomes very slow and one can feel like VMD is not working. It does not slow...
07 August 2017 639 10 View
Is there anything like universal 3 letter code for sulfonated tyrosine like other usual amino acid residues
07 August 2017 4,196 2 View
Hi all, Is there a way to find consistent hydrogen bonds in between sidechain-sidechain, backbone-backbone residues in gromacs? Can I point out some residues and plot a graph wherein I can see...
07 August 2017 1,508 4 View
Suggestions regarding Protonation prediction servers apart from H++., PDB2PQR and Reduce!
04 May 2017 3,135 4 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
I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...
04 August 2024 1,200 2 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
Please suggest basic literature on lattice-based cryptography. A kind response from the cryptographic community will be highly appreciated.
24 July 2024 6,291 4 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