[gmx-users] Re: high repulsion in packed system

Vitaly Chaban vvchaban at gmail.com
Sun Jul 11 12:18:16 CEST 2010

In "PE60-3.75nm3.gro" enlarge the box size. Then use NPT simulation to
compress the MD box.

Dr. Vitaly Chaban

> 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.

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