[gmx-users] Combining various Flat-bottomed Potentials
jagannath mondal
jm3745 at columbia.edu
Wed May 25 07:44:45 CEST 2016
Hi
I am also interested in the issue of using a flat-bottomed restraint,
for a spherocylinder.
However, I am not sure whether the current gromacs settings of even a
linear combination of a sphere and cylinder can help here to generate a
spherocylinder.
If we put the spherical and cylindrical restraint on the same particle
(under the [position restraints] flag as Justin and Chris has suggested ),
the particle will be either be in a spherical confinement or in a
cylindrical confinement . But for a spherocylinder, we need two
hemispheres which are capped on the two ends of a cylinder.
Hence, for a spherocylindrical restraint, what is needed here is a
restraint which will restrain the particle on going out when the z
coordinate of the particle exceeds the diameter of the cylinder AND the
sqrt(x**2+y**2) of the particle exceeds the length of the cylinder.
I am wondering whether this is possible within the current gromacs
implentation.
If it is not, I was interested in editing the source code relevant for flat
bottomed potential, to implement it for a spherocylinder. Is the following
path within gromacs directory right place to make the changes ?
gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c
Any suggestions will be welcome.
Thanks
Jagannath
On Wed, May 25, 2016 at 2:22 AM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:
> Thanks for the clarification Justin.
>
> Those interested in using these potentials (as I was) should be careful as
> I think that at lease some forms are broken when using domain decomposition:
> http://redmine.gromacs.org/issues/1969
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin
> Lemkul <jalemkul at vt.edu>
> Sent: 24 May 2016 12:33:54
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Combining various Flat-bottomed Potentials
>
> On 5/24/16 12:30 PM, Christopher Neale wrote:
> > I doubt it. The flat-bottom potential in the pull-code is not really the
> standard definition of a flat-bottom potential. In my opinion, a
> flat-bottom potential has a low, and a high defined value and then the
> restraint increases harmonically above high and below low with no penalty
> between low and high set values. However, the gromacs 5.1.2 flat-bottom
> potential is simply a regular potential where the forces are set to zero
> below the central set point and there is a harmonic above the central set
> point. I'd call this a half-harmonic rather than a flat-bottom potential.
> Luckily, the code is quite simple to modify to get a proper flat-bottom
> potential, which you could use to get your cylinder.
> >
> > You want to modify src/gromacs/pulling/pull.cpp around line 1129 and
> remove the code:
> >
> > if (pcrd->params.eType == epullFLATBOTTOM && dev < 0)
> > {
> > dev = 0;
> > }
> >
> > And replace it with:
> >
> > if (pcrd->params.eType == epullFLATBOTTOM)
> > {
> > if (dev > -1 && dev <1){
> > dev = 0;
> > } else {
> > if (dev >0){
> > dev-=1;
> > }else {
> > dev+=1;
> > }
> > }
> > }
> >
> > That will give you a flat-bottom width of 2.0 nm (1 nm on each side).
> This is the quick and dirty approach where you just hard-code your
> potential flat-bottom width then compile it like that. You will need to
> change the "1" in four places if you want a different width.
> >
>
> If I understand the OP correctly, this isn't a matter of using the pull
> code,
> rather simultaneously using flat-bottom options in [position_restraints].
> It
> should be possible to simply combine the available options to whatever the
> user
> desires. Several people have asked the same question in recent days, yet
> it
> doesn't seem like anyone's actually *tried* to do it yet. That would be a
> much
> more useful effort :)
>
> -Justin
>
> > Obviously test it also prior to production.
> >
> > 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 Srajan
> Jain <sr.j240 at gmail.com>
> > Sent: 24 May 2016 05:13:17
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] Combining various Flat-bottomed Potentials
> >
> > Dear Gromacs users,
> >
> > I want to impose a sphero-cylinderical position restraint, using
> > flat-bottomed potentials, for a simulation.
> >
> > The manual mentions that we can combine the existing three flat-bottomed
> > potentials, like a cylinder with two layers to get a disk.
> >
> > So, can this feature be used to generate a sphero-cylinder?
> >
> > Thank you in advance.
> > --
> > Gromacs Users mailing list
> >
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>
> --
> ==================================================
>
> 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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