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-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Srajan Jain
<sr.j...@gmail.com>
Sent: 24 May 2016 05:13:17
To: gromacs.org_gmx-users@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.
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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
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