[gmx-users] Combining various Flat-bottomed Potentials

Christopher Neale chris.neale at alum.utoronto.ca
Tue May 24 22:07:00 CEST 2016

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){
                      }else {

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.

Obviously test it also prior to production.

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.
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