[gmx-users] Errors during pull constrained NPT simulation for permeability calculations.

[Christopher Neale]

Dear Yogesh:


you either need to make the system larger in the dimension(s) of your pulling or you need to not pull out to such a far distance. Once you straighten that out, and if the lincs problems remain, then we can tackle that separately.


What are your mdp options for pulling? Maybe you really only care about Z dimension pulling but you are actually pulling in XYZ and that could have some effect on largest distance vs box size? I presume that if you pull only in Z and you have large Z but small X and Y that the simulation will not complain, but I don't remember.

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of jay patil <jpatil911 at gmail.com>
Sent: 15 June 2017 09:18:39
To: gmx-users at gromacs.org
Subject: [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.

Hi Experts,
I am doing simulation for permeability calculation.
  In my simulation, water molecule is constrained (inside the Bilayer) at fixed distance from centre of the Bilayer. And another constrained in bulk water. I am doing equilibration with V-rescale(thermostat) and berendsen(for barostat) for 5ns and then production run with Nose-Hoover and parrinello-Rahman for 15ns. Simulation is crashing during production run after few nanoseconds run.
Sometimes I get error "distance between pull group 1(Bilayer COM) and 3(water) is large than 0.49 times the box size. You might want to consider using 'pull-geometry =direction-periodic' instead "
  But I cannot use direction-periodic in NPT.
  Sometimes I get error, "water molecule starting at atom XXX can not be settled."
   I observed, these XXX water molecules are not constrained one's  but they are from bulk water surrounding Bilayer.
Question:
  1. What is alternative for "pull-geometry=distance" if my constrained molecule going outside the box due to volume fluctuations, since we cannot use direction-periodic in NPT.
  Molecule is constrained around 1nm inside the initial box boundary.
  2. What might be the reason for instability in bulk water which is SPC.
  3. If there is distortions in Bilayer during pulling, leading to overlap, simulation would have crashed in initial stages, why it is crashing in later stages.

  Any helpful tips, suggestions will be much appreciated.

Yogesh
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