[gmx-users] Dummy Problem.
acb15885 at uprm.edu
Wed Feb 7 14:48:45 CET 2007
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
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???
On Tuesday 06 February 2007 8:08 pm, Mark Abraham wrote:
> Anthony Cruz wrote:
> > Hi Users:
> > In my topology before all the bonded information I add the following
> > lines with the appropiate numbers:
> > [ dummies2 ]
> > ;Dummy from funct a
> > CON ND OE 1 0.064381
> > [ constraint ]
> > ; ai aj funct b0
> > ND OE 2 0.12032
> > The problem is that the dummy colapse with the ND atom during the EM.
> > What could be the problem? I need to add the dummies2 section in my
> > topology if it is present in the residue topology and it is present in my
> > pdb???
> Does it work without the constraint?
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