Position restraints freezes unrestrained molecule also

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GROMACS version: 2021.3
GROMACS modification: No
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I am using Martini FF to model sorption of a polymer on a surface in CG water. The shape of the surface is maintained with position restraints applied in x, y and z direction (FC = 1000 in the 3 directions). However, after running for 500 ns production run, the polymer molecule also seems to be frozen.

If I simulate the polymer molecule alone in water (in the absence of the position-restrained surface), the molecule undergoes significant conformation changes in less that 10 ns. However, when combined with position-restrained surface, the polymer conformation does not change at all even after 500 ns. I looked at the trajectory video and it appears that some of the beads in the polymer chain were “vibrating” at their positions but did not move (the expected coiling and wagging motion of polymer chain was absolutely absent).

In the gro file, the surface has atom no. 1-2700 (these are followed by polymer starting from 2701 and then water beads). The posres.gro and posres.itp correspond to the first 2700 atoms/beads only. Hence, the position restraints are applied only to the surface.

I have energy minimized the system, then NVT equil followed by NPT with Berendsen and then NPT with Parinello-Rahman. NVT and NPT equil were performed with 10 fs/step for 0.5 ns each. This is followed by production run for 500ns under NPT with Parinello-Rahman barostat. The -DPOSRES was used at all steps, from minimization to production run. The surface structure will collapse within 0.5 ps in the absence of position restraints so these are indispensable.

Can someone please let me know why the polymer is not changing its position and conformation when combined with the position-restrained surface. And, is there a way to fix this?

Thanks!
RPS

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Hi,

Could it be that you apply position restrain also to the polymer?

POSRES is a pretty standard label used in the topology file to call for the position restrain.
You can check if you have the following definition in the polymer topology at the end of the [ moleculetype ] definition for the polymer

; Include Position restraint file
#ifdef POSRES
#include “xxxx.itp”
#endif

If it is the case, you can change the name of POSRES in something else.

I hope it helps
Alessandra

3

Dear Alessandra,

Thank you for the reply.

I found that this was due to the “freezing” issue often reported with Martini water on surfaces. The problem was resolved by increasing the temperature to around 300K and adding antifreeze water.

Thanks again!
RPS