[gmx-users] Scaling of Coordinates is Occurring - why?

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Jan 16 18:50:31 CET 2010

 From what I can find, it seems that you are correct to assume that  
frozen coordinates should not be scaled:  
and, from the online manual:

     Groups that are to be frozen (i.e. their X, Y, and/or Z position  
will not be updated; e.g. Lipid SOL). freezedim specifies for which  
dimension the freezing applies. To avoid spurious contibrutions to the  
virial and pressure due to large forces between completely frozen  
atoms you need to use energy group exclusions, this also saves  
computing time. Note that frozen coordinates are not subject to  
pressure scaling.

Nevertheless, you say that your frozen coordinates are subject to  
pressure scaling. I can suggest the following:

1. Are you really freezing what you think you are freezing? I see no  
freeze info in your post so I can't check for myself. i.e. do you have  
proper freezegrps? did you utilize freezedim? did you include  
energygrp_excl (which, although required, shouldn't affect frozen atom  
scaling if you forgot it). Note that your refcoord_scaling only  
matters if you are using position restraints, which you say you are not.

2. Just use position restraints with a large force constant and use  
that refcoord_scaling = no.

3. If you're absolutely sure, file a bugzilla.

-- original message --

Pressure coupling is not supposed to scale the coordinates of my frozen
group, yet it is.  My frozen group is a crystal structure that does not have
any topology assigned to them: no bond, angle, dihedral constants etc.
specified.  I find that a crystal structure gets compressed.  A sample of
the pressure coupling section of my .mdp file is given below:

pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 50.0
compressibility = 0.1 0.1 0.1 0.1 0.1 0.1
refcoord_scaling = no
ref_p = 1000.0 1000.0 1000.0 0.0 0.0 0.0

I'm using Gromacs 4.0.5.
Any suggestions appreciated,

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