[gmx-users] Justin biphasic tutorial with controlled adsoption of protein
jalemkul at vt.edu
Sun May 3 18:29:04 CEST 2015
On 5/3/15 9:07 AM, James Lord wrote:
> Hi Justin,
> Thanks for the info, your assumption re long axis of the box is correct (z),
> here is the .gro file I have for one the oil (decane)-protein (the protein is in
> the middle part of the free space above the oil surface). Is that what you were
> talking about? I went through manual and could not get what to do for position
> restrains, appreciate if you can elaborate further on it? Thanks for your final
> point re solvent/ions separate coupling.
Restraints require a reference coordinate for each atom to which restraints are
applied. Normally this is read from -c when running grompp (useful for absolute
restraints), but the origin of the restraint can be replaced with a reference
position in -r. If you're trying to restrain a molecule to some region of space
(what you're trying to do here), you basically need to define some coordinate
along the axis/axes of interest that defines a boundary for the potential. If
you're trying to restrict motion along z, then the z-coordinates of all the
atoms to which restraints are applied need to be set to this value. The
coordinate file passed to -r is thus not physically the coordinates of the
molecule, but defines a reference location at which the restraints are applied.
This is also useful for doing, e.g. osmotic pressure calculations - you can
restrain ions within a certain region of space and the waters can move freely; a
virtual semi-permeable membrane. Could be a useful toy system for you to debug
any issues you might run into.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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