[gmx-users] CONSTRAINED SIMULATIONS

[chris.neale at utoronto.ca]

Dear Giuseppe:

This is a pretty good example of how it can be useful to completely  
describe what you are doing at first posting. What you mention could  
easily be a problem for a couple of reasons:

1. The manual indicates that you may need more than one shake  
iteration in this case (or at least it seems possible that this case  
is included in what the manual says, although I admit that it is vague):

Constraint forces The distance between the centers of mass of two  
groups of atoms can be constrained and the constraint force monitored.  
The distance can be in 1, 2, or 3 dimensions. This method uses the  
SHAKE algorithm but only needs 1 iteration to be exact if only two  
groups are constrained.

2. The manual also says:

constraint forces can only be calculated between groups that are not  
connected by constraints to the rest of the system. If a group  
contains part of a molecule of which the bondlengths are constrained,  
SHAKE or LINCS and the constraint force calculation here will  
interfere with each other, making the results unreliable. This means  
that for simulations with constraints = all-bonds in the .mdp file  
pulling is limited to whole molecules or groups of molecules. In some  
cases this limitation can be avoided by using the free energy code,  
see sec. 6.3.

Now I know you say angle restraint, not angle constraint, but again  
this complicates the issue.

So:

1. remove the angle restraint and see if the constraint force works as  
expected
2. if it does, add back the angle restraint while increasing the  
number of shake iterations (I have no idea how you could do that).


Chris.


-- original message --

I don't think it is something related to pbc because my solutes are well
inside the simulation box (as I told you before I visualize them via a movie
while the simulation proceeds).

Nor it is something related to the barostat because I saw that warning
and in order to try to see it work I decided to do NVT simulations.
However, the problem persists.

I'm using angle restraints on the "pulled" group in order to preserve its
orientation with respect to the reference group. Could this be the problem?

Cheers,

  Giuseppe



Constraint forces The distance between the centers of mass of two  
groups of atoms can be
constrained and the constraint force monitored. The distance can be in  
1, 2, or 3 dimensions.
This method uses the SHAKE algorithm but only needs 1 iteration to be  
exact if only two
groups are constrained.