[gmx-users] pr_md

[K.A. Feenstra]

David van der Spoel wrote:
> On Fri, 13 Dec 2002 ehab at biof.ufrj.br wrote:
> 
> 
>>David,
>>
>>I'm running the 3.1 version of GROMACS e my minimization work out...but I've 
>>got the same message of LINCS warning...I'm confuse too.
>>Could be something else?
> 
> If you do EM do you have constraints turned off? (you should...)

I often first EM without constraints (i.e. flexible bonds), and then
another EM with constraints turned on, and then MD with position restraints
(and constraints on).

You also could have a problem if you position restrain the minimized
structure to the non-minimized starting structure, i.e. like

grompp -c after_em.gro -r b4_em.gro


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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