[gmx-users] constraints and pbc=full

[Yang Ye]

Malin Bergenstrahle wrote:

> Hi,
>
> I am trying to simulate a system of infinite cellulose chains by using 
> pbc=full.
>
> As far as I have understood from the list this option cannot be used 
> together with any bond constraints. Is this correct? It is possible to 
> run simulation with the constraints, but I guess something becomes false.
>
> This seems to be a problem for me, because I have a couple of 
> hydrogens that seem to get unreasonable high energy and start 
> rotating; i.e. I would like to use constraints=hbonds.

You may use CVS version for pbc=full with lincs. SHAKE is not 
implemented yet.

>
> If anyone has any suggestion about what I could do instead of 
> constraining the h-bonds, or any idea about what could possibly be 
> wrong I would be mostly grateful.
>
> /Malin
>
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