[gmx-users] Polymer in periodic boundary conditions again

[K.A. Feenstra]

Ester Chiessi wrote:
> Hi all,
> 
[...]
 >
> In another test, I repeated the same calculation but without introducing the
> connectivity in the topology file. The run chrashed again, with a constraint
> error in algorithm Lincs at step 1. In the step0.pdb output file some atoms
> of the chain ends are far off the box.
> 
> Then I tried the following (with a topology without explicit connectivity).
> Before starting the dynamics, I minimized the energy of the system to relax
> the water, by constraining the polymer chain at the aim to mantain the
> orientation for the periodicity. After this calculation the chain ends
> diverged a little. The following dynamics seems to go, but the chain ends
> move without periodicity.
> 
> In each trial I used: setenv GMXFULLPBC 1.
> 
> Where is the mistake?

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.

Are you using pressure coupling? This might also disrupt your periodic
connectivity.


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "If You See Me Getting High, Knock Me Down"               |
|        | (Red Hot Chili Peppers)                                   |
|________|___________________________________________________________|