<br clear="all">Hello everyone,<br><br>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. <br>
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<pre class="western" style="font-weight: normal; text-align: justify;">genconf -f PE60-3.75nm3.gro -nbox 1 4 2 -o PE60-3.75nm3-nbox142.gro<br><br>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. <br>
<br>Any suggestions is appreciated.<br><br><br>Potential Energy = 1.22210418131690e+08<br>Maximum force = 1.23807588295471e+07 on atom 364<br>Norm of force = 1.82513032084293e+06<br><br><br>******************************************************em.mdp<br>
<br>constraints = all-bonds<br>integrator = steep ; use cg for conjugate gradient<br>dt = 0.002 ; ps ! not necessary for EM, only needed for dynamics integrator like MD<br>
nsteps = 40000 ; 200 in minimization runs, this is just the max no. of iterations<br>nstlist = 10 ; frequency to update neighbor list. updates every 10 steps<br>ns_type = grid<br>
<br>rlist = 1.0 ; cut-off distance for short-range neighbor list<br>rcoulomb = 1.0 ; distance for coulomb cut-off<br>rvdw = 1.0<br><br>; Energy minimizing stuff<br>
<br>emtol = 1000.0 ; minimization converges when max force is smaller than this value, in units of KJ/mol.nm<br>emstep = 0.01 ; initial step-size
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