[gmx-users] Re: lincs error

[K.A. Feenstra]

hugo verli wrote:
> 
> Dear Anton,
> 
> I obtained a lincs "error" previously described here (I reproduced the entire
> message). Your "trick" worked pretty fine.
> However, this error occurred in the termalization step and proceeds to the
> molecular dynamics itself. Is there any problem if I use the 6 decimal places in
> a full precision .trr since the beginning of the simulation? Some property of my
> simulation could be altered?

You can apply the same trick in the middle of a simulation. It still is
a bit of cheating, but not actually wrong. You simply introduce different
rounding errors (there are always rounding errors, of course). It is in
some sense the same as running on a different type of hardware, that will
also have different roundof errors... In general, if you apply the trick
once, and your 'error' goes away, it is all right. If it recurs, especially
if it recurs in the same location and/or recurs frequently, there is 
probably something wrong, e.g. a strange conformation or wrong parameters.

> The problem occur always in a sulphonamide group. It appear to be correlated to
> the rotational movement of sulphone around nitrogen atom.

In that case, you might want to review the parameterization of this group.
You could modify angle or (improper) dihedral parameters to make the group
more stable (in the simulation). In all likelihood, this will not be so
important for the 'proper' physical behaviour of the group, but if this is
an important group (i.e. e..g. involved in/close to active site) be sure 
to check it well!


-- 
Groetjes,

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