[gmx-users] Chains blowing Apart

[Xavier Periole]

On Mon, 26 Nov 2007 13:45:01 +0530 (IST)
  csreddy at ncbs.res.in wrote:
> Hi All,
> I have been trying run energy minimization for a homoTRIMER protein, I
> have puzzled by the following results!
> 
> 1) energy minimization in vacuum 1 chain is separated from the remaining 2
> chains. I tried for 5 models in 4 models chains are separated and one is
> normal.
>
> 2)energy minimization in box with or with out solvent, no chain separation
> for all the 5 models.
> please note that EM method is steepest decent, I have tried size on the
> box up to 20nm.

you are probably experiencing the effect of PBC. In the cases you
see "separation", centering the protein in the box should solve the
problem.


> CONTESTS OF MDP FILE
> 
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> nsteps              =  100
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  2000
> emstep              =  0.01
> 
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1
> rcoulomb            =  1.0
> rvdw                =  1.0
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> 
> 
> What would be the probable reason for this. Please let me know.
> 
> Regards
> Chandu
> 
> 
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------