FW: [gmx-developers] Free Energy Calculation

[Anton Feenstra]

On 02/09/10 04:58, Emanuel Birru wrote:
> Hi,
>
> I am doing a partition coefficient of solute between 1-Octanol and water
> using gromacs ffG53a6 force field. Actually I am trying to reproduce
> Garrido et al’ s paper (J. Chem Theory Comput. 2009). The first thing I
> have done is to predict the Gibbs free energy of salvation of pentane
> (my solute) in 1-Octanol by thermodynamics integration method using 16 λ
> (lambda) values. It works well for λ =0. 0.05, 0.1, 0.2, 0.3, 0.4 and
> 0.5. The problem has stated at λ=0.6 and it is LINCS error which says as
> follows:
>
> Fatal error:
>
> Too many LINCS warnings (1001)
>
> If you know what you are doing you can adjust the lincs warning
> threshold in your mdp file or set the environment variable
> GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem
>
> The atoms that make the problem are pentane atoms.

Do you have angle constraints on your pentane? Lincs cannot handle 
highly connected constraints, like the linked triangles you get with 
bonds and angles constrained in pentane.

(However, I do not know how this could explain that #1 of your sc_alpha 
runs *does* work.)


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Free University  Amsterdam     |
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