[gmx-users] MD of a crystall structure

[Mark Abraham]

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