[gmx-users] Freeze groups, energy group exclusions and partially frozen dihedrals

Jennifer Williams Jennifer.Williams at ed.ac.uk
Thu Nov 5 15:49:26 CET 2009

I have two questions about Freeze groups

I have a large residue made up of SiO2 (like quartz). I also have  
organic surface groups (imagine a propyl chain) which are anchored to  
the surface of my large silica structure.

I have decided to freeze my silica structure (all silicons and  
oxygens) in all 3 directions. I do this :
1. to save computational time,
2. because its movement in relation to the other moving parts of the  
system is not significant
3. because although I have obtained some parameters for Si-O bending  
etc-these were not parametrized for this particular system)

My topology file currently contains parameters for Si-O bending,  
O-Si-O stretching etc (i.e those parts of the molecule I now wish to  
freeze). I thought that if I used the freeze parameter, that these  
parameters would be ignored and not contribute to the total potential  
energy. (Indeed someone replied to my last post saying that this was  
the case and it would be OK to leave them in). This is not the case as  
I have found large differences in energy if I leave these parameters  
for the frozen parts in or not. So I now assume I have to remove the  
parameters which define completely frozen parts of my residue.

Question 1.

I have read that I should use energy group exclusions on the frozen  
part of my molecule. However, I only achieve a neutral structure if I  
consider the charge on both the frozen and non-frozen parts of my  
molecule (I can?t change the charges to make the frozen part neutral).  
In fact if I try to exclude the frozen group, I get the following  

WARNING 1 [file SIL.top, line 28748]:
   Can not exclude the lattice Coulomb energy between energy groups

I assume this is because to ignore the charges on my frozen part would  
leave me with a large overall charge.

If I continue with the energy group exclusion (but allowing the  
coulombic energy to be calculated) I get:

Steepest Descents converged to Fmax < 200 in 144 steps
Potential Energy  = -2.5177378e+05
Maximum force     =  1.9338353e+02 on atom 4084
Norm of force     =  1.5444931e+01

Without excluding the frozen energy group I get:

Steepest Descents converged to Fmax < 200 in 154 steps
Potential Energy  = -1.4675300e+06
Maximum force     =  1.7721352e+02 on atom 4084
Norm of force     =  1.4064426e+01

Either one looks reasonable to me. I can?t decide which is the most  
sensible option. Does it make more sense to use energy group  
exclusions (with the exception of coulombic terms) or to go without  
excluding groups at all.

Question 2

I am a bit mixed up about what to do when I have flexible surface  
groups (i.e not frozen) anchored to a frozen surface-specifically  
about what to do for constraints, bonds, angles and dihedrals which  
connect a frozen molecule/s to moving one/s.

e.g If all Silicons and Oxygens are frozen, does it make sense to  
include the following in my topology file.


Si ? C  (where Si is frozen)


Si ? C   (where Si is frozen)


O ? Si - C  (Si and O  atoms frozen)

Si ? C - C  (Si  atom frozen)


Si ? O ? Si - C   (3 atoms of dihedral frozen)

O ? Si ? C - C    (2 atoms of dihedral frozen)

Si ? C ? C - C     (1 atom of dihedral frozen)

My feeling is that I still need to include these parameters to define  
how the flexible surface groups move. Does anyone know if this will  
give spurious results because part of the molecule is frozen.?

I'd really appreciate any advice because this has been confusing me  
for some time.


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