[gmx-users] refcoord-scaling

Tue Apr 8 23:56:32 CEST 2014

Thanks, Mark. I actually ran the same system with "com" option for timestep
of 1 fs using latest gromacs version 4.6.5 (earlier version i used was
4.6.3) and interestingly, it's running fine, not at all blowing up.
Thanks
Chetan

On Tue, Apr 8, 2014 at 2:43 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Apr 8, 2014 12:14 AM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:
> >
> > Hi,
> >
> > Thanks a lot. It is clearer, but I have questions, so this email:
> >
> > Why is option "none" not desirable, if we want to restrain positions of
> > atoms of crystal to specific points? Isn't the strain generated due to
> > atoms scaling but not reference coordinates helping?
>
> Only if the model can absorb that stress at the given time step, which
> might not be true with heavily coupled constraints.
>
> > Why is none option
> > better than "com"? Is the possible movement of crystal due to "com"
> option
> > desirable?
>
> I already offered a theory about com not working in your case.
>
> > If a particular option exists, then it does so for a particular purpose.
> In
> > which case, "none" or "all" be a valid option?
>
> These are all unphysical hacks, so "it was easy to implement and might be
> useful enough for something" is a valid purpose when building a general
> purpose tool. Probably protein use cases were considered, and not crystal
> structures. Do something that works and move on to real equilibration! :-)
>
> Mark
>
> > Thanks
> > Chetan
> >
> >
> > On Mon, Mar 24, 2014 at 10:40 PM, Christopher Neale <
> > chris.neale at alum.utoronto.ca> wrote:
> >
> > > Say you have a box with an x-side length of 3 nm and two atoms with
> > > x-dimension position restraints to: (a) x=1 nm, and (b) x=2 nm
> > >
> > > Then let the box shrink to 99% of its previous size due to pressure
> > > coupling. The following is my understanding of  the locations to which
> the
> > > atoms will be restrained:
> > >
> > > refcoord_scaling =
> > >
> > > none:
> > > (a) x=1 nm, and (b) x=2 nm  -- note how the restraint positions are not
> > > scaled (even though the positions of the atoms are scaled due to
> pressure
> > > coupling)
> > >
> > > all:
> > > (a) x=0.99 nm, and (b) x=1.98 nm   -- note how the atoms are now
> > > restrained to be closer together
> > >
> > > com:
> > > (a) x=0.985 nm, and (b) x=1.985 nm  -- note how the distance between
> the
> > > atoms is maintained
> > >
> > >
> > > So you see how "none" leads to problems because the restraint reference
> > > positions are not scaled at all with the atomic positions and how "all"
> > > leads to problems because, if you restrained all Ca atoms, then you
> would
> > > get compression/expansion of the size of your protein as the system
> > > fluctuated in constant pressure simulations.
> > >
> > > Chris.
> > > ________________________________________
> > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Chetan
> > > Mahajan <chetanvm10 at gmail.com>
> > > Sent: 24 March 2014 23:25
> > > To: gmx-users at gromacs.org
> > > Subject: Re: [gmx-users] refcoord-scaling
> > >
> > > Thanks, Justin. I am trying to understand what is meant by 'com'
> option.
> > > Following two sentences in manual seem conflicting with each other:
> > >
> > > "*Scale* the center of mass of the reference coordinates with the
> scaling
> > > matrix of the pressure coupling. The *vectors of each reference
> > > coordinate*to the center of mass are *not
> > > scaled*."
> > >
> > > Doesn't scaling center of mass of reference coordinates change
> something
> > > else ? reference coordinates?
> > >
> > > Thanks
> > >
> > > Chetan
> > >
> > >
> > > On Mon, Mar 24, 2014 at 8:22 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > >
> > > >
> > > >
> > > > On 3/24/14, 9:05 PM, Chetan Mahajan wrote:
> > > >
> > > >> Hi Justin,
> > > >>
> > > >> My system is TiO2 crystal (2160 atoms position restrained) solvated
> by
> > > >> 3656
> > > >> water molecules, 1 formate anion and 1 sodium ion.  Is it true that
> when
> > > >> 'all' option is used, positions of the atoms (meant to be
> restrained)
> > > >> always change?
> > > >>
> > > >>
> > > > Consider what position restraints are doing.  They never guarantee
> that
> > > > atoms won't move; they just apply a biasing potential to disfavor
> > > movement.
> > > >  So yes, your atoms will probably move.  The smaller the system, the
> > > larger
> > > > the effect will likely be.  Consider also what reference coordinates
> are
> > > > doing.  They define how strong the potential is (distance between
> current
> > > > coordinates and reference).  If you're scaling all atoms individually
> > > > according to the pressure coupling, the reference moves and therefore
> the
> > > > atoms can also move.  For larger systems like proteins,
> > > "refcoord_scaling =
> > > > com" is normal and stable, and "refcoord_scaling = all" is
> disfavored.
> > > >  Honestly, I don't know what to expect for a very small system like
> > > yours,
> > > > but it is likely to be affected to a greater extent.
> > > >
> > > > If the "all" option gives you a stable simulation that allow for
> proper
> > > > equilibration, then I doubt there is any real problem.
> > > >
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==================================================
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > > >
> > > > Department of Pharmaceutical Sciences
> > > > School of Pharmacy
> > > > Health Sciences Facility II, Room 601
> > > > 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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