Hello everyone, I am trying to energy minimize a system of 8 polyethylene molecules with 60 units. In literature density of PE is reported 0.9 gr/cm3. Based on this I need to have each single chain in 3.3 nm^3. If I put this chain in a box of 15*0.5*0.5 =3.75 nm^3 I am close to the density I want.
genconf -f PE60-3.75nm3.gro -nbox 1 4 2 -o PE60-3.75nm3-nbox142.gro Now I have 8 molecules but these long chains are very packed and I get very large repulsive potential after EM.I increased nsepts to 4000 but still I have problem ( I tried different integrator algorithms as well). Later I want to work with chains much longer than 60 units and system becomes even more packed. Any suggestions is appreciated. Potential Energy = 1.22210418131690e+08 Maximum force = 1.23807588295471e+07 on atom 364 Norm of force = 1.82513032084293e+06 ******************************************************em.mdp constraints = all-bonds integrator = steep ; use cg for conjugate gradient dt = 0.002 ; ps ! not necessary for EM, only needed for dynamics integrator like MD nsteps = 40000 ; 200 in minimization runs, this is just the max no. of iterations nstlist = 10 ; frequency to update neighbor list. updates every 10 steps ns_type = grid rlist = 1.0 ; cut-off distance for short-range neighbor list rcoulomb = 1.0 ; distance for coulomb cut-off rvdw = 1.0 ; Energy minimizing stuff emtol = 1000.0 ; minimization converges when max force is smaller than this value, in units of KJ/mol.nm emstep = 0.01 ; initial step-size
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