[gmx-users] MD of a crystall structure
Mark.Abraham at anu.edu.au
Fri Mar 4 08:07:19 CET 2011
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.
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