[gmx-users] high repulsion in packed system

Moeed lecielll at googlemail.com
Sun Jul 11 08:23:24 CEST 2010

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


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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