Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

Justin A. Lemkul wrote: ERIKSSON, EMMA wrote: I was using those "strange" values of tau_p and compressibility to keep the z box length fixed in order to avoid problems associated with scaling the positions of the molecules in the box when we constrain the distance between DPPC and the smal

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0e-14 compressibility =

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

jalem...@vt.edu] Skickat: den 29 april 2010 17:20 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: > Pcoupl = Parrinello-Rahman > pcoupltype

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

ERIKSSON, EMMA wrote: Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0e-14 compressibility = 4.5e-5 4.5e-15 I would bet almost anything that this is the cause of your problem. How did you come up with these bi

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

___ Från: gmx-users-boun...@gromacs.org > [gmx-users-boun...@gromacs.org] för Justin A. Lemkul [jalem...@vt.edu] > Skickat: den 29 april 2010 15:28 Till: Gromacs Users' List Ämne: Re: > [gmx-users] Constrained simulations crash when bilayer moves in the z > direction in the b

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

...@gromacs.org [gmx-users- boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and li

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

] för Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 15:28 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: The last section of my mdp file:

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

A. Lemkul [jalem...@vt.edu] > Skickat: den 29 april 2010 14:33 Till: Gromacs Users' List Ämne: Re: > [gmx-users] Constrained simulations crash when bilayer moves in the z > direction in the box > > ERIKSSON, EMMA wrote: >> My system consists of 128 lipids and 3655 wate

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

s-boun...@gromacs.org <mailto:gmx-users-boun...@gromacs.org>] för XAvier Periole [x.peri...@rug.nl <mailto:x.peri...@rug.nl>] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z di

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

t; Emma >> >> *Från:* gmx-users-boun...@gromacs.org [gmx-users- >> boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] >> *Skickat:* den 27 april 2010 16:32 >> *Till:* Discussion list fo

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

den 29 april 2010 14:09 > Till: Discussion list for GROMACS users > Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in > the z direction in the box > > Do you have sufficient water on either "side" of your membrane? That is, are > the lipid

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

XAvier Periole [x.peri...@rug.nl <mailto:x.peri...@rug.nl>] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

#x27;t understand you explanation. >> >> Emma >> >> >> >> *Från:* gmx-users-boun...@gromacs.org >> <mailto:gmx-users-boun...@gromacs.org> [gmx-users-boun...@gromacs.org >> &l

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

romacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

Avier Periole [x.peri...@rug.nl <mailto:x.peri...@rug.nl>] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the p

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

] för Justin A. Lemkul [jalem...@vt.edu] Skickat: den 27 april 2010 15:37 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: > Hi again, > Thanks Xavier for your reply. I

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

XAvier Periole [x.peri...@rug.nl] Skickat: den 27 april 2010 16:32 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

idn't understand you explanation. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] Skickat: den 27 april 2010 12:41 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in t

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

ROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of yo

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

trained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to