[gmx-users] molecule breakage during minimization

[Yogesh Sharma]

Hello everyone,
Before equillibriation I was trying to minimize my protein membrane system.
energyminimized.gro file  when vizualized in vmd showed few lipid molecules
broken. Is it safe to use trjconv to make whole molecule after em or i can
proceed with breakage? This is the minimization.mdp file I am using
define                  = -DREST_ON -DSTEP6_0
integrator              = steep
emtol                   = 1000.0
nsteps                  = 5000
nstlist                 = 10
cutoff-scheme           = Verlet
rlist                   = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
coulombtype             = pme
rcoulomb                = 1.2
;
constraints             = h-bonds
constraint_algorithm    = LINCS