[gmx-users] problem with tutorial KALP-15 in DPPC

Hi all I'm doing the GROMACS tutorial KALP-15 in DPPC. I've done the steps until the energy minimization, so now I've my system at an energy minimum and I'm doing the equilibration with this nvt.mdp: define = -DPOSRES ; position restrain the protein and lipid ; Run parameters

Re: [gmx-users] problem with tutorial KALP-15 in DPPC

On 2/3/14, 12:10 PM, serena wrote: Hi all I'm doing the GROMACS tutorial KALP-15 in DPPC. I've done the steps until the energy minimization, so now I've my system at an energy minimum and I'm doing the equilibration with this nvt.mdp: define = -DPOSRES ; position restrain the

Re: [gmx-users] problem with tutorial KALP-15 in DPPC

step 0: Water molecule starting at atom 101831 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I would suggest you to do one more round of minimization by taking the final minimized .gro file and then perform a short simulation with a time step of 0.5 fs.