GROMACS version: GROMACS modification: Yes/No Here post your question I want to pull the ligand from protein in negative y axis. I have also made changes in script and added pullvec coordinates as 0 -1 0 but still it pull.mdp (2.1 KB) s pulling positive direction of axis. What could be the solution? 1 post - 1 participant Read full topic

GROMACS version: 2020.2 GROMACS modification: Yes Hi, I am trying to keep 13 separate 1nm sized dye molecules aggregated by pulling each molecule towards the center of mass of all groups. By indexing all atoms of all 13 groups as a 14th group called 13Dyes, I tell gromacs in the mdp file to individually pull each dye molecule towards group 14. However, no matter how large my box…

GROMACS version: GROMACS modification: Yes/No Here post your question gmx dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc -o dssp_1.dat -xvg xmgrace unable to plot dssp.dat file 1 post - 1 participant Read full topic

GROMACS version:2023.4 hello developers. im compiling Gromacs-2023.4 with cp2k-2023.2，and the GNU complier used is gcc-11.4 installed by cp2k toolchain.I successfully installed GROMACS (with some extended versions like double precision and MPI) and CP2K separately, but encountered problems when using libcp2k.a to install GROMACS with QM/MM functionality support. My installation co…

GROMACS version: 2020.1-Ubuntu-2020.1-1 GROMACS modification: No Here post your question Hello, I was working on my MD simulation of a MgO nanoparticle generated from CHARMM-GUI. I was running it in multiple steps of 20ns, and after the first step, when I was checking the results, my nanoparticle started to deform: (not letting me upload my images because i’m a new member) I …