GROMACS version:4.5.3 GROMACS modification: Yes Why do we want the residue to be protonated, if it’s pka value is close to the ph we want to simulate in? 1 post - 1 participant Read full topic

GROMACS version: GROMACS modification: Yes/No Here post your question while running the following command gmx grompp -f em.mdp -c 1_ions.gro -p topol.top -o em.tpr i am getting the following issue WARNING 1 [file topol.top, line 104856]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with l…

GROMACS version: GROMACS modification: Yes/No Here post your question while perfoming following command: gmx mdrun -v -deffnm em i am getting this: WARNING: Listed nonbonded interaction between particles 9647 and 9657 at distance 2.413 which is larger than the table limit 2.050 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule y…

Hi, All When I ran gmx mdrun -v -deffnm em step for my apoprotein md analysis, I got the following error I used workstation which has no gpu features. I got a doutbt whether there is any problem in gormacs installation? Could anyone kindly rectify my error? 1 post - 1 participant Read full topic

GROMACS version: 2021.6-Colvars-2022-12-16-dev GROMACS modification: No Here post your question Hi all, I have performed a metadynamics simulation with the Colvars module; I decided to stop it before it got to the final step. In the simulation I biased three CV’s and I have the pmf file for each variable: I was wondering if there is a tool to “reconstruct” a 2d pmf having the 1…

GROMACS version: 2022.4 GROMACS modification: Yes/No While installing gromacs, in the section"make check" I receive 1 test error, can anyone help me how to solve it??? Thanks in advance! 99% tests passed, 1 tests failed out of 88 Label Time Summary: GTest = 631.46 secproc (81 tests) IntegrationTest = 326.84 secproc (25 tests) MpiTest = 534.37 secpr…