[gmx-users] Distance Restraints

[Andrea Hombrecher]

Dear GROMACS-Users!

The description of the distance restraint options on pages 64-67 of the
manual is not completely clear to me. When I include the following
distance restraints into the topology

[ distance_restraints ]
;ai        aj        type    index   type'   low     up1     up2     fac

892      4879    1        0          1        0.30     0.30    0.60
1.0
947      4879    1        1          1        0.30     0.30    0.60
1.0
2816    2850    1        2          1        0.30     0.30    0.60
1.0
3544    4849    1        3          1        0.30     0.30    0.60
1.0
4192    4850    1        4          1        0.30     0.30    0.60
1.0
4228    4880    1        5          1        0.30     0.30    0.60
1.0
4834    4888    1        6          1        0.50     0.50    0.80
10.0
4834    4906    1        7          1        0.18     0.18    0.50
10.0

And I set the following options in the mdp-file

disre                    = Simple
disre-weighting   = Equal
disre-mixed         = no
disre-fc               = 1000
disre-tau             = 0
nstdisreout           = 100

Does it mean that fc = 1000 kJ/mol/nm^2 is

a) devided by the number of pairs (8) and each potential is then
multiplied by the factor, or

b) devided by the number of pairs considering the factor (26), or

c) is it devided only within pairs with the same index number (no
devision in this case)?

When I set

disre                    = Simple
disre-weighting   = Conservative
disre-mixed         = no
disre-fc                = 1000
disre-tau              = 0
nstdisreout            = 100

Is it right that every pair gets fc = 1000 kJ/mol/nm^2 multiplied by the
factor?

What makes more sense for

a) restraining hydrogen bonds in a protein (pairs 0-5 in the example
above)

b) restrainig the distance between an enzyme and a substrate defined in
the same topology file (pairs 6 and 7 in the example above)?

Can I define two separate distance restraint files for these two
different cases in the same topology file?

Thanks in advance for help,  I'm really confused about this subject!

Andrea


--
Andrea Hombrecher

Heinrich-Heine-Universitaet Duesseldorf
Institut fuer pharmazeutische Chemie
Gebaeude 26.23
Universitaetsstrasse 1
40225 Duesseldorf

   Tel: 0211-81-13830
   Fax: 0211-81-13847
E-mail: hombr at pharm.uni-duesseldorf.de