up from version 4.6.7 and above.
Not natively, but I think you can do it with PLUMED.
Hi, An energy minimization step I converged to machine precision with the following values: Potential Energy = -5.0373220e+06 Maximum force = 1.1988365e+03 on atom 6641 Norm of force =...
08 April 2023 3,039 2 View
Hello, I'm trying to understand photon shielding parameters such as mass attenuation coefficients (MAC's) and effective atomic numbers (Zeff's). I would like to ask how to calculate for total...
08 April 2020 8,259 2 View
I'm looking for some research (article) about Agrobacterium tumefaciens live shelf at the plant cells after infection? After infection, the ti-DNA is transferred to the plant cell and genes are...
16 December 2019 3,980 10 View
Hello everyone, I' trying to simulate a system with multiple chains. According to the PDB entry, there is a single disulfide bond connecting two of the chains. Unfortunately, 'pdb2gmx' with '-ss'...
18 June 2019 6,791 2 View
I have a question about Agrobacterium tumefaciens transmission. Is there any publication that Argobacterium can be transmitted by air or by dust particles in greenhouses?
20 November 2018 9,416 3 View
Hi everybody. I'm looking for extracted DNA from Curtobacterium flaccumfaciens pv. poinsettia bacteria for positive control. Does someone has it or can tell me there I can get it? Thanks.
02 April 2017 4,077 1 View
Hi, I'm looking for a DNA sequence for identification of Xanthomonas axonopodis pv. begoniae. Does someone has this information? Or any article that may help me to find specific primers for this...
13 June 2016 6,463 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
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