[gmx-users] Polymer in periodic boundary conditions again

Ester Chiessi ester.chiessi at uniroma2.it
Thu Nov 21 17:02:19 CET 2002

Hi Anton and all,


K.A. Feenstra wrote:

> You might try the following (which is what I intended to say in the
> first place):
> 1) energy minimze your non-inifinte polymer.
> 2) Probably the end points will no longer be 'periodically aligned'
>     at the box edges; correct that by rotation and/or adjusting the
>     size of the box (I expect your molecule to shrink a little).
>     You might have to remove some water (or, throw away your water and
>     use genbox again).
> 3) switch to the 'explicitly connected' (i.e. infinite) topology and
>     energy minimize again.

I followed the instructions.

The log file of the step 3) says:
Removing pbc first time.
There were 2 inconsistent shifts. Check your topology.
Done rmpbc.
The minimization goes on and the final structure seems OK.

I found in the mailing list archive:


There the warning 'inconsistent shifts. Check your topology.' was related a some
corruption of the trr file.
What in my case?
I revised my topology and it likes good.



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

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