[gmx-users] Position restraint problem

[Arpita Aravind]

Hi David,
Thank you for your reply. 
On performing energy minimization the potential energy
decreases from ~ 5e+09 kJ/mol to -1e+06 kJ/mol, hence
one would assume that all bad Van der Waals contacts
are removed. However, after energy minimization, on
performing a short MD with position restraint on the
heavy atoms and using 'gmxcheck' to analyze the
trajectory file, a large number of carbon atoms are
printed out. I have listed a few of them below:

atom# name  residue r_vdw  atom# name  residue r_vdw 
distance
   77   CG HISA   8 0.15      81  CE1 HISA   8 0.15  
0.2183
   80  CD2 HISA   8 0.15      81  CE1 HISA   8 0.15  
0.2193
  184   CG  TRP  21 0.15     190  CE2  TRP  21 0.15  
0.2335
  185  CD1  TRP  21 0.15     187  CD2  TRP  21 0.15  
0.2255
  185  CD1  TRP  21 0.15     190  CE2  TRP  21 0.15  
0.2284
  269   CG HISA  28 0.15     273  CE1 HISA  28 0.15  
0.2168
  272  CD2 HISA  28 0.15     273  CE1 HISA  28 0.15  
0.2189 

As can be observed from above, the distance between
the atoms is less that the sum of both their Van der
Waals radii. I cannot understand the cause for this.
Thank you.
Regards,
Arpita.
 
--- David <spoel at xray.bmc.uu.se> wrote:
> Are you sure? This would mean huge vanderwaals (LJ)
> energies. Could it
> not be something with visualisation?
> 
> 
> -- 
> Groeten, David.
>
________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept.
> of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://zorn.bmc.uu.se/~spoel
>
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