[gmx-users] DUMMY and CONSTRAINED

[David van der Spoel]

On Wed, 2004-04-21 at 14:18, acorrea at unisa.it wrote:
> 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.

OK, I think I understand. You do have to remove those bonds. If the
dummy is defined correctly it will be at the right position anyway.

> 
> 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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> 
> 
> 
> 
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-- 
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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