[gmx-users] about "LINCS WARNING"

[Anton Feenstra]

...
>      I am trying to simulate the interface between alkyls &
> water, the decane (C10 , declared in ffgmx.itp) and SOL (OPLS)
> are used. 

First, you cannot mix force fields. If you use the ffgmx forcefield
for your alkanes, you must use SPC (or SPCE) water, since that is
what has been used when deriving the other ffgmx forcefield parameters.
If you want to use OPLS water, you must also use OPLS parameters for
your alkanes.

Second, if you want to minimize some more, you are better of using
flexible waters. The constraints algorithms used for bond lengths
and angles make it harder to minimize the energy. So, you should
add that line define = -DFLEX_SPC back into your .mdp file.

Third, mdrun must optimize the step length for energy minimization,
simply because when the step is too large, energy will go *up* in
stead of down.

Fourth, I notice you use a 0.0001ps time step (i.e. 0.1 fs). As
counterintuitive as that may seem, a very small step can also give
rise to problems, which are related to the precision of the calculations.
A step size below 1 fs should not be necessary for any normal mdrun.

Finally, I agree with Kun-Lin in that you probably have some problem
in your initial conformation, e.g. overlap between atoms. I suggest
you review the procedure by which you generate your starting coordinates.
Ofcourse, if you explain to us what you did, we might help... ;-)


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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