From what I can find, it seems that you are correct to assume that
frozen coordinates should not be scaled:
http://lists.gromacs.org/pipermail/gmx-users/2002-July/002054.html
and, from the online manual:
freezegrps:
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:
; PRESSURE COUPLING
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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