We need a few more details, do you only want to know how to modify and/or turn on position restraints, or how to calculate adequate values for your purpose?

Hello Mary,

I have been trying to resolve following issue.

I have been utilizing BUMPy [Article BUMPy: A Model-Independent Tool for Constructing Lipid Bilay...] to create the semi sphere plane of two different lipids DPPC and POPC. To fix the curvature, we have DUMY wall which only interact with hydrophobic part of lipids.I have gone through minimization, equilibration and production steps using default gromacs process available in charmm.gui. My simulation is losing it's curvature configuration after 120ns, I want to run it for several microseconds. Also, DUMY wall is interacting with the system and contributing to lipid system. We need to fix this wall in it's initial setup.

To fix the curvature with DUMY, we have martini_DUMMY itp file with code: In martini_dummy.itp file: 

.....................................

   #ifdef DUMMY

          [ position_restraints ]

    1 1 1000.0 1000.0 1000.0

    #endif 

To address this, we have included following code in the .mdp file of minimization, equilibration and production of gromacs files.

define = -DDUMY_POS_RES

We tried three different options.

(i) with pressure coupling

(ii) with freeze grps

(iii) without pressure coupling

I've never used BUMPy and don't work with lipids, but on brief inspection it appears there are multiple sources of potential instability. For one, it forms curved surfaces from flat monolayers, which could produce instability through clashes within the bilayer. In that case, if you have numerical instabilities you could run a short energy minimization with soft-core potentials first (weaker nb interactions).

Another potential issue could come from the high level of curvature for the semi-sphere. If you have the option, you could do a test run on a system with less curvature to see if the mapping from a flat surface to the more highly curved semi-sphere generated by BUMPy is too unstable for your system.

Also, instead of using the dummy particles/wall, you could just position restrain the phosphates.

Finally, looking over briefly, I'm not finding any all-atom simulations that used BUMPy beyond 50 ns to test for stability. If it turns out that the method isn't stable for long runs in all-atom, you could build with CHARMM-GUI instead with artificial pores and long equilibration.