[gmx-users] DUMMY and CONSTRAINED

[acorrea at unisa.it]

Hallo,
 
> Did you make the topology yourself?

Yes I made the topology on myself but the  system is small (68 atoms without
solvent box).
I tried the option -normdumbds in this way:

grompp -f run.mdp -normdumbds -c confout.gro -p topol.top -o topol.tpb

and I found the same error:
Cleaning up constraints and constant bonded interactions with dummy particles
ERROR: Cannot have constraint (1-27) with dummy atom (27)
ERROR: Cannot have constraint (11-28) with dummy atom (28)
ERROR: Cannot have constraint (10-28) with dummy atom (28)
ERROR: Cannot have constraint (9-28) with dummy atom (28)

etc. etc.

In the run.mdp file I put:

constraints              = all-bonds
; Type of constraint algorithm =
constraint-algorithm     = Shake
; Do not constrain the start configuration =
 unconstrained-start      = no
; Relative tolerance of shake =
shake-tol                = 1e-04

I think that the rilevant bit of my topology is this:

[ dummies3 ]
; Dummy from   func         a          b
27  4  2  6    1         0.275725314  0.275725314
28  9  7 11    1         0.275725314  0.275725314

[ bonds ]
; ai  aj  funct    c0      c1
    1   27    1   0.213800 9.2004000e+04
    1   28    1   0.213800 9.2004000e+04
    1   13    1   0.228000 9.2004000e+04
    2    3    1   0.140000 3.3456000e+05
    2    6    1   0.140000 3.3456000e+05
    2   21    1   0.094000 3.1365000e+05
    2   27    1   0.119000 2.5092000e+04
    3    4    1   0.140000 3.3456000e+05
    3   24    1   0.094000 3.1365000e+05
    3   27    1   0.119000 2.5092000e+04
    4    5    1   0.140000 3.3456000e+05
    4   12    1   0.187000 2.0910000e+05
    4   27    1   0.119000 2.5092000e+04
    5    6    1   0.140000 3.3456000e+05
    5   23    1   0.094000 3.1365000e+05
    5   27    1   0.119000 2.5092000e+04
    6   22    1   0.094000 3.1365000e+05
    6   27    1   0.119000 2.5092000e+04
    7   11    1   0.140000 3.3456000e+05
    7   17    1   0.094000 3.1365000e+05
    7   28    1   0.119000 2.5092000e+04
    7    8    1   0.140000 3.3456000e+05
    8    9    1   0.140000 3.3456000e+05
    8   18    1   0.094000 3.1365000e+05
    8   28    1   0.119000 2.5092000e+04
    9   10    1   0.140000 3.3456000e+05
    9   12    1   0.187000 2.0910000e+05
    9   28    1   0.119000 2.5092000e+04
   10   20    1   0.094000 3.1365000e+05
   10   28    1   0.119000 2.5092000e+04
   10   11    1   0.140000 3.3456000e+05
   11   19    1   0.094000 3.1365000e+05
   11   28    1   0.119000 2.5092000e+04
   12   25    1   0.130000 1.8400800e+05
   12   26    1   0.130000 1.8400800e+05
   13   14    1   0.110000 2.5928400e+05
   13   15    1   0.110000 2.5928400e+05
   13   16    1   0.110000 2.5928400e+05

Thank you again







> There is an option -normdumbds in grompp that you could try. If it
> doesn't work send the relevant bit of the topology to the list.
> 
> By the way, do check the resulting tpr file (gmxdump -s)
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
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