[gmx-users] Position restraint problem

[K.A. Feenstra]

Arpita Aravind wrote:
> Hi,
> I am trying to perform MD simulation on my protein
> consisting of chains A (451 residues) and B (444
> residues) and neutralized by 46 NA+ ions. On
> performing "gmxcheck" on the the trajectory file
> obtained after the short MD with position restraint, I
> find that a large no. of heavy atoms like the carbon
> atoms are overlapping (i.e. the average distance
> between them is less than the sum of both Van der
> Waals radii). 
[...]

After seeing David's replies, I feel there still is some
explaining to do. 'gmxcheck -c' does a very rough check on
atom overlap. If I saw it correctly in your list, all the
overlapping atoms are bonded to each other, or have only
two intervening bonds (i.e. one bonded atom in between).
That means that the close distances are most probably
quite OK. 'gmxcheck -c' simply does not take the topology
information into account when checking.


-- 
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)                                   |
|________|___________________________________________________________|