[gmx-users] MD of polymer in pbc

[K.A. Feenstra]

Ester Chiessi wrote:
 > Hi Gromacs people,
 >
 > I'm working to perform molecular dynamics simulations of a polymer in PBC and I
 > found some problems.
 >
 > After preliminary minimizations and preparations of the system (with no problem if
 > I don't insert the connectivity accross boundaries), I received this message during
 > the minimization of the 'infinite' chain:
 > ...........
 > Removing pbc first time.
 > There were 2 inconsistent shifts. Check your topology.



[...]
 > Step -2, time -0.004 (ps)  LINCS WARNING
 >  atom 1 atom 2  angle  previous, current, constraint length
 >       1      2   88.9    0.1527   0.4141      0.1530
 >      38      1   97.4    0.1510   1.0500      0.1530
[...]
 > Step -1, time -0.002 (ps)  LINCS WARNING
 >  atom 1 atom 2  angle  previous, current, constraint length
 >       1      2  105.5    0.4141   0.2115      0.1530
 >      38      1   96.1    1.0500   0.0735      0.1530
[...]

You have bonds that should be 0.15 nm in length, but they vary
from 0.07 (half what it should be) to 1.05 (seven times too large).
That is serious. My first assumption would still be what I
suggested before: your polymer conformation is not minimized
well enough. It should first be minimized as a *finite* molecule,
to remove all internal strain, and subsequently as an *infinite*
molecule, in combination with adjusting the box dimension. But,
by now you probably did that already. My only remaining advice
is to check all the steps that you did up to now (i.e. look at all
the intermediate structures, check the bonds and angles by hand,
using e.g. rasmol, etc.), and hope that someone else on the list
with experience in infinite molecules can help you further... ;-)

-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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