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

[jay patil]

Thanks Christopher for the answer. Will take the bigger system and see if it works. Thanks.

Yogesh

> On 16-Jun-2017, at 12:24 AM, Christopher Neale <chris.neale at alum.utoronto.ca> wrote:
> 
> 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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