[gmx-users] Warning: Short Bond pdb2gmx

Dear Gromacs users I did 50ns MD simulation of a protein-ligand complex. From this trajectory, I extracted region of trajectory having stable rmsd and generated an average structure. I want to run this average structure to get an idea of setting some restraints. but when I do gmx pdb2gmx I get

[gmx-users] dssp 3.1.4

Good day, I have recently downloaded the latest dssp version and with the mkdssp executable file as I type chmod +x dssp and run this code : gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg -tu ns the process starts but no output is created after even 1 day my

Re: [gmx-users] PBC after energy minimization

Hi Mohamed, > Hello everybody, > > In order to solve the PBC at the end I use the command: > > *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * > > followed by: > > *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* > > > I want to solve this problem after the energy

[gmx-users] conformation tensor

Dear all, I like to calculate the conformation tensor for a mass of a short polymer. The conformation tensor is defined as c_ij = 3* ( / <(Re_bulk)^2>), in which Re_i and Re_j are the Cartesian components of the Re as the end-to-end vector. Several gmx options are available to calculate the