[gmx-users] distance between atoms of system and periodic image

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 10 07:55:42 CET 2005

On Thu, 2005-02-10 at 12:29 +0100, Ester Chiessi wrote:
> Hi.
> I'm considering a polymer network in water and I'd like to simulate a
> 'infinite' periodicity by covalently binding the tail of a chain with the
> periodic image of its head. The network has been built with one infinite
> chain in the x direction, a second infinite chain in the y direction and a
> third in the z direction, to have an omogenoeous system.
> The problem is that the distance between the atoms to be linked (across the
> boundary) is too long in the starting structure and it's not possible to
> perform the energy minimization as the bond energy is very high ( water
> molecules cannot be settle ......etc).
> What is the simplest way to obtain the right position of the atoms?
Do it in vacuum or do it using free energy tools, making the bond length
slowly go from whatever it is to a normal bond. Notice that you have to
use pbc=full for infinite molecules, and you can not use constraints on
the polymer.

> Sorry for my quite 'anomalous' questions and thanks in advance.
> Ester
> Ester Chiessi
> Dipartimento di Scienze e Tecnologie Chimiche
> Università di Roma Tor Vergata
> Via della Ricerca Scientifica
> 00133 Roma
> tel. +39 06 72594462
> fax  +39 06 72594328
> http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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