[gmx-users] MD of a crystall structure

Hernan Ahumada hernan at chem.gla.ac.uk
Thu Mar 3 14:41:52 CET 2011

Dear users

I am trying to make  MD of a crystal structure of carborane. This molecule is a
ridge cage of 12-vertex (C2B10H12). I have all the bonding and non-bonding 
parameter from amber and I am working with this condition, for LJ interaction
using sigma and epsilon

 [ defaults ]
; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
  1		2		yes		0.5 	0.8333

I am using compresibility of 5 × 10-6 bar-1, mimicking conditions of zero
surface tension, I think for a solid is OK, Is not it? . I am a bit confusing,
I am using LINCS constraints for  all bonds but the simulation stop after 300ps
with LINCS problems.  "LINCS WARNING relative constraint deviation after LINCS "

The simulation stop because the system is not well equilibrated.
When I work without Domain Descomposition the dynamics is more stable, but when
I use constraints equal none or Hbonds the dynamics it is  stable. The question
When  have I to change the type of constrains?

Thanks for help me with this problems

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