On 4/03/2011 12:41 AM, Hernan Ahumada wrote:
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?
See manual 7.3.18 for relevant info.
Mark
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