[gmx-users] Justin biphasic tutorial with controlled adsoption of protein

Justin Lemkul 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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