[gmx-users] cg warning

Nuno R. L. Ferreira nunolf at ci.uc.pt
Tue Jun 8 16:22:48 CEST 2004

On Monday 07 June 2004 04:39 pm, Derrick Guang Yuh Lee wrote:
> dear gmx-users
> i attempted to run an energy minimization with integrator = cg and
> constraints = all-bonds, and i keep getting the following error:
> ---------------------------------------------------------------
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> ERROR: constraints with Conjugate Gradients not implemented
> Generated 1174 of the 2016 non-bonded parameter combinations
> Excluding 3 bonded neighbours for DPPC    40
> Excluding 2 bonded neighbours for SOL   1448
> processing coordinates...
> double-checking input for internal consistency...
> ERROR: can not do Conjugate Gradients with constraints (4856)
> Fatal error: There were 2 errors
> ---------------------------------------------------------------
> and was curious what does this mean and how can i deal with it?

Have you tryed cg + constraints = none ?

> additionally, could someone explain to me in a little detail the
> significant difference between setting constraints between none and
> all-bonds?

The constraints are used to maintain some properties, like bond lenghts and 
angles, within a meaningfull interval, defined in the f.f.
Check the manual, chapter 3.6

 i've been assuming that with all-bonds, the water molecules
> angles are constraint such that the angle between the H bonds are the
> same. thank you in advance.
>  - derrick
>  derrick Lee
>  faculty of Science
>  Memorial University of Newfoundland
>  k24dgyl at mun.ca / derrickglee at hotmail.com
> "a teacher is never a giver of truth - he is a guide, a pointer to the
> truth that each student must find for himself. a good teacher is merely a
> catalyst."
>                                                               - bruce lee
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Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica 
Departamento Química
Universidade de Coimbra
"Do not worry about your difficulties in maths.
 I can assure you that mine are still greater."

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