RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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 a

RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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 incorrect. I wanted to multiply the margin

RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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: [gmx-users

RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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

Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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

Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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

RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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. While looking at the code again

Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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

RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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])

RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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

RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

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