[gmx-users] about minimization

[Anton Feenstra]

David van der Spoel wrote:
> 
> On Thu, 21 Mar 2002, hugo verli wrote:
> 
> >sorry if I am introducing problems already discussed before in this list. But I
> >wasn`t able to resolv it yet and I did not found teh answer in the list files. I
> >read some references in wich the gradient used to normal mode analysis is under
> >10e-5 kcal. But I cannot achieve gradient under 10e+2 kj, neither with steepest
> >descents or with conjugated gradients. I reproduced these erros and one answer
> >here. But I am working with double precision so the problem still exist. I also
> >tried to minimize another system (I choosed the speptide.pdb from gromacs
> >tutorial). The error with this structure is the same. Could these errors be dued
> >to my machine or am I doing something wrong?
> 
> I have looked into this last week or so, and it may be that something is
> wrong with the conjugate gradients minimizer. I haven't found the real
> problem yet.

Is it possibly a problem with constraints? The default Gromacs parameters
will turn bonds into constraints and constrain those using Lincs, also
during EM. But for CG/NM type of calculation, the default 4th order for
Lincs is not sufficient. In that case, try 8 or 12...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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