Hi,
OK, so you have a stable simulation and the box corrections are caused by
"diffusion"
of the box shape. This diffusion issue has been solved for Gromacs 4.0, where
with
isotropic scaling the box shape is fixed.
But the actual problem causing the crashes has not been found yet.
I tried with
Hi,
I am also starting to wonder now if you might have other problems.
Have you checked if there aren't very strong volume fluctuations?
Could you mail your mdp pressure coupling parameters?
Berk.
> Date: Thu, 27 Mar 2008 15:16:39 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> S
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
Date: Fri, 7 Mar 2008 10:14:00 +0100
> Date: Thu, 6 Mar 2008 13:57:31 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re
> Date: Thu, 6 Mar 2008 13:57:31 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
>
> Berk Hess a écrit :
> > Hi,
> >
> > I now realized that my fix what completely
Berk Hess a écrit :
Hi,
I now realized that my fix what completely incorrect.
I wanted to multiply the margin of 0.0001 by 2, not the factor 0.5.
But my mistake means that is now given an error when the off diagonal
element is relatively more than 1 instead of more than 0.5.
This is a far too we
Hi,
I now realized that my fix what completely incorrect.
I wanted to multiply the margin of 0.0001 by 2, not the factor 0.5.
But my mistake means that is now given an error when the off diagonal
element is relatively more than 1 instead of more than 0.5.
This is a far too weak check.
So I would n
Berk Hess a écrit :
Is the fix committed already, i cannot get it from the current cvs
repository?
Cheers,
Stéphane
Yes, it is: revision 1.57.2.7 of pbc.c.
It just adds "2*" in front of BOX_MARGIN.
Berk.
ok, found, forgot to add the 3.3 branch tag...
Thanks for the fix.
--
Stéphane Téle
> Date: Wed, 20 Feb 2008 12:01:59 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
>
> Berk Hess a écrit :
> >
> > That good news.
Berk Hess a écrit :
That good news.
While looking at the code again just now,
I realized what the actual problem is.
The check before and after the box correction are both done with BOX_MARGIN,
which can lead to the problem you observed when the last bit of the box
is rounded in an unlucky fash
All occurrences of BOX_MARGIN in pbc.c should have the factor of 2:
#ifdef ALLOW_OFFDIAG_LT_HALFDIAG
else if ((fabs(box[YY][XX])+fabs(box[ZZ][XX])> 2*BOX_MARGIN*box[XX][XX]) ||
(fabs(box[ZZ][YY])> 2*BOX_MARGIN*box[YY][YY]))
#else
else if ((fabs(box[YY][XX])> 2*BOX_MARGIN*box[XX]
That good news.
While looking at the code again just now,
I realized what the actual problem is.
The check before and after the box correction are both done with BOX_MARGIN,
which can lead to the problem you observed when the last bit of the box
is rounded in an unlucky fashion. So even with you
> Date: Mon, 28 Jan 2008 15:29:28 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
>
> Dear Gromacs-users,
>
> I have been performing simulations with cubic and octah
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