[gmx-users] Dummy Problem.

[Mark Abraham]

Anthony Cruz wrote:
> Hi Mark:
> Thank you for your interest. No, it does not work without the constraint.  the 
> dummy atom still collapsing with the ND atom.  Also I try:
>  [ constraint ]
>  ;  ai  aj funct           b0 
> ND      CON	  2	   0.064381
> 
> But grompp give me the following error:
> Cleaning up constraints and constant bonded interactions with dummy particles
> ERROR: Cannot have constraint (86-87) with dummy atom (87)
> Fatal error: There were 1 dummy atoms involved in constraints

OK, that's expected behaviour if you read the relevant manual section.

> Also I try to put all the [ dummies2 ] and [ constraints ]  after the bonding 
> information with the same result, the collapsing of the dummy atom.
> 
> What could be the problem???

I'm guessing wildly here, but maybe EM doesn't work with dummy atoms. 
Try an EM without the dummy atom and then do position restrained MD with 
the dummy atom and see how you go.

Mark