[gmx-users] Brownian dynamics]

[Michel Fodje]

I didn't find any clashes or flying atoms/bonds in the configuration. 
However, I just repeated the process with just the protein and no Zn
ions and I get a different error message


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 4.942302 (between atoms 3138 and 3139) rms 0.529467
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      1      2   90.0    0.1000   0.1062      0.1000
      1      3   31.9    0.1000   0.0992      0.1000
      7      8   90.0    0.1000   0.1245      0.1000
...
Wrote pdb files with previous and current coordinates

So I checked both files, step-1.pdb looks okay but step0.pdb looks
strange -- hydrogen atoms are flying all-over the place and main some
aromatic rings are severely twisted. According to the manual lincs_order
should be 8 for BD which it is!


On Wed, 2002-02-13 at 18:34, David L. Bostick wrote:
> Perhaps there is some bond missing in your topology.  Can you dump out a
> configuration and look at it graphically?  If you see something flying
> away, then maybe you can pinpoint the problem.
> 
> David
> 
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> David Bostick					Office: 262 Venable Hall
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> 
> On 13 Feb 2002, Michel Fodje wrote:
> 
> > 
> > > That is a pretty undeniable indication that there is something
> > > seriously wrong with your starting structure: the 'outer' two atoms
> > > of a series of four bonded atoms (A1 and A4 in A1-A2-A3-A4) should
> > > normally be no further than 3 times your average bondlength apart,
> > > say roughly 3*0.15 nm = 0.45 nm, not nearly 1 nm...
> > 
> > I have done minimization before the dynamics.  
> > My starting structure is an X-ray structure with 5 ZN2+ ions placed
> > randomly within a 1nm thich shell that is at least 1nm from the surface
> > of the protein;
> > This is the procedure I use:
> > 
> >  - pdb2gmx : gromos vacuumm force field
> >  - grompp with em.mdp  -"-
> >  - mdrun em
> >  - mdrun bd
> > 
> > Running mdrun with -debug option does not give any extra information.
> > 
> > 
> > Thanks for all the help,
> > 
> > Michel
> > 
> > 
> > 
> > 
> > 
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