chris.ne...@utoronto.ca wrote:
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.
This is a known problem. The options freezing and pressure coupling are
not compatible. Ref_coordscaling refers to position restraints, see
http://manual.gromacs.org/current/online/mdp_opt.html#pc
There is no general solution for this, since pressure scaling may make
the box so small that the frozen system is larger than the box (the same
problem holds for position restraints by the way).
We would like to do this rigorously but as far as I know no-one has
worked out a solution.
It gets more complicated when constraints are involved.
-- 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,
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
