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

Ester Chiessi ester.chiessi at uniroma2.it
Fri Feb 11 12:37:19 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.

Thanks a lot for your help.

I'd prefer to keep water, if possible.
I thought to use the pull_code and to adjust a single chain one at a time.

This is my pull.ppa file, for the infinite connectivity in the z direction.
The idea is to zero the x and y components of the distance between the
first and last atom, to obtain the alignment along z.

verbose = no
runtype = constraint
pulldim = Y Y N
Skip steps = 10
group_1 = a_557   ;the last atom of the chain
reference_group = a_1     ;the first atom of the chain
;constraint_direction = 1 1 0 ;;;;;; I can't really understand the difference
;;;;in using: pulldim or:  constraint_direction
constraint_rate = -0.1

Then I'll go to adjust the distance along z (to obtain the box size) with a
following run, using:
pulldim = N N Y

Do you think it could work?

I'm wondering whether it is possible to obtain the same result in a single


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

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