GROMACS version:2020.6 GROMACS modification: No 1.Why changes in rlist happen when I run the same thing in a GPU vs CPU? 2.I have set the r-list and nst-list value in the parameters files , yet why they change. And do these changes has any impact on the results? GPU gmx mdrun -deffnm complex_nvt -v -nt 64 Reading file complex_nvt.tpr, VERSION 2020.2-dev-20200430-5e78835-unk…

GROMACS version: 2019 GROMACS modification: Yes/No Here post your question I want to calculate distance between centroids of Tyr and Trp. Can I use center of geometry for this? I don’t know how exactly GROMACS describes COG and if it would be appropriate for residues like TRP. 1 post - 1 participant Read full topic

GROMACS version: 2019.6 GROMACS modification: No Hi all, I am currently running tests on reproducing the calculation of a protein in vacuum that was run using the amber14sb forcefield. I am writing the topology manually and comparing to the one where I run calling the forcefield itself. I know this seems redundant, but it will be important for my future work. I have a pair list…

GROMACS version: 2021.4 GROMACS modification: No I am interested in returning to some simulations run a few years ago by a visiting student; specifically, I would like to run some variations in temperature and pressure. All I have is a .tpr file, albeit one that can be successfully executed by Gromacs to produce the expected output. I can use gmx dump to save this into a text fi…

GROMACS version: 2021.4 GROMACS modification: No Here post your question Able to install gromacs in windows using ubento , but not able to install gromacs in Linux VM ( cantos )… Anyone came across this issue please share the install procedure 1 post - 1 participant Read full topic

GROMACS version: 2021 GROMACS modification: Yes/No Dear GROMACS users, I am trying to run a MD for a complex containing a protein, a ligand, ADP and Mg2+ ions. charmm36-feb2021 force field has been employed. [assuming that like ATP, the parameters for ADP are also predefined in charmm36-feb2021] This is the error I am getting: Program: gmx pdb2gmx, version 2021.2 Source f…

GROMACS version: 2020.5 GROMACS modification: Yes/No While treating pbc using gmx trjconv -s prod.tpr -f prod.xtc -o nopbc.xtc -pbc mol -center, gromacs throws me these warnings and so on - There were 162 inconsistent shifts. Check your topology There were 162 inconsistent shifts. Check your topology There were 162 inconsistent shifts. Check your topology time 100.000 There…