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

James Lord jjamesgreen110 at gmail.com
Mon May 4 04:29:40 CEST 2015

Hi Justin,
I definitely saw this in the manual but as I said before couldn't get the
part "a suitable [position_restraints] " and "negative force constant" in
your earlier email. Would you please let me know the right way of doing
this? may be an example of the command etc to be used?

On Mon, May 4, 2015 at 4:28 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> 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
> http://mackerell.umaryland.edu/~jalemkul
> ==================================================
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