[gmx-users] Polymer in periodic boundary conditions again

Ester Chiessi ester.chiessi at uniroma2.it
Mon Nov 18 11:07:08 CET 2002

Hi all,

> It might be simply a combination of a non-optimized starting structure with
> your infinite polymer chain. Have you tried to start an 'explicitly connected'
> simulation using the energy-minimized starting conformation that you described?
> You would probably have to re-adjust the x-dimension of your box to get the
> ends of your polymer to line up at the box edges again. You might also need
> or want to re-minimize the system after adjusting the box.

My work for building a polymer in periodic boundary conditions is going on.
Thanks a lot!

Starting from the chain in the water box (by genbox), with an 'explicitly
connected' topology, I minimized (freely) the energy till emtol 1000. The final
structure seems o.k. but the chain doesn't perfectly fit the x axis: it results
translated along X and some last atoms are out of the box. mdrun output says, from
the beginning,
There were two inconsistent shifts. Check your topology

Can I consider the minimization correct?

My idea is to 'correct' the coordinates of the polymer by translation of the right
amount and to repeat the minimization.

Are there any suggestion?

Thank you very much,


Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462

More information about the gromacs.org_gmx-users mailing list