[gmx-users] Slab gets bended in NVT

paul buscemi pbuscemi at q.com
Sat Jul 28 22:43:57 CEST 2018


NPT appears to be doing exactly what it should esp if your slab is a membrane

1) are you using pcoupltype = surface tension  with compressability  =  4.5e-5   0  ??  

2) have your tried  xy restraints on the ends of the slab


> On Jul 28, 2018, at 5:10 AM, Alex <alexanderwien2k at gmail.com> wrote:
> Dear all,
> In modelling a slab and some molecules on top of it, the slab gets bended
> (Fig.2) during the NVT production or equilibration simulations while I do
> NpT equilibration (berendsen followed by Parrinello-Rahman) long enough
> (Fig.1) so that the box parameters, pressure and energies are stable enough
> prior staring the NVT one.
> Fig1: After around 2 ns NpT equilibration
> https://drive.google.com/open?id=1lhDruLuSx0Qf5DT4cIriTX3uoi5w_AVS
> Fig2: During NVT
> https://drive.google.com/open?id=1CyDBrM1Ks52ViG8fh0_pnoClqymJVjGg
> The slab got equilibrated separately before I bring it to the new system
> and even I restrain the slab's atoms to their equilibrated initial
> positions using "7000 7000 5000" spring constants in X,Y and Z directions,
> respectively.
> The point is that the problem does not happen in a smaller (laterally
> around 7nm*7 nm) slab, but it happens when I use a larger slab (laterally
> around 20nm*20nm).
> Above I have shared two pictures of the system, would you please share your
> thoughts about the issue?
> Thank you.
> Regards,
> Alex
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