Hi Berk, some of my simulations crashed again, basically with the same error message:
"Source code file: ns.c, line: 313 Fatal error: Could not correct too skewed box" Right now I have factored all occurrences of BOX_MARGIN by 2 in src/gmxlib/pbc.c but kept the original value of 0.5001 for BOX_MARGIN in include/pbc.h. Could the bug maybe fixed by setting BOX_MARGIN to 0.5005 while multiplying all instances in src/gmxlib/pbc.c by 2? Best Luther > 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][XX]) || > (fabs(box[ZZ][XX])> 2*BOX_MARGIN*box[XX][XX]) || > (fabs(box[ZZ][YY])> 2*BOX_MARGIN*box[YY][YY])) > > You can leave BOX_MARGIN at 0.5001. > > All these things are not critical for correct results. > The only annoying thing is that the "old" 3.3 code can give a fatal error > due to a rounding issue. > > Berk. > >> Date: Thu, 14 Feb 2008 14:31:15 +0100 >> From: [EMAIL PROTECTED] >> To: [email protected] >> Subject: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling >> Hi Berk, >> thanks again. I am not sure though whether I have understood what modifications you have suggested. In src/gmxlib/pbc.c there are several occurrences of BOX_MARGIN, some with and some without a factor of two. Should each occurrence be multiplied by two (so those that have the factor >> already are left as they are and all others get multiplied)? Could you post the lines 71 to 76 of src/gmxlib/pbc.c with the right corrections so >> that I can be sure to implement them correctly? >> Also, should I leave the value for BOX_MARGIN in include/pbc.h at 0.5005 >> or change it back to 0.5001 ? >> Best >> Luther >> > 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 your change the problem >> > could still occur. >> > A real fix is adding a factor 2 (2*) in front of BOX_MARGIN in src/gmxlib/pbc.c. >> > I have added this fix for the 3.3.3 release. >> > >> > Berk. >> > >> >> Date: Wed, 13 Feb 2008 16:37:55 +0100 >> >> From: [EMAIL PROTECTED] >> >> To: [email protected] >> >> Subject: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling >> >> >> >> Hi Berk, >> >> >> >> the change of parameter worked! My simulation finished without >> crashing. >> >> >> >> >> >> Thanks for your help >> >> >> >> Luther >> >> >> >> >> >> >> Dear Gromacs-users, >> >> >> >> >> >> I have been performing simulations with cubic and >> octahedron-shaped >> >> >> boxes >> >> >> using Parrinello-Rahman pressure coupling. After some time I get >> the >> >> >> error >> >> >> message "Could not correct too skewed box" and the simulations >> crash. >> >> >> I set the parameters for the coupling as listed below: >> >> >> >> >> >> pcoupltype = isotropic >> >> >> tau_p = 5.0 >> >> >> compressibility = 5e-5 >> >> >> ref_p = 1.0 >> >> >> >> >> >> >> >> >> I have never encountered the same problems when using Berendsen >> >> pressure >> >> >> coupling so I suppose I must have made a bad choice for some >> >> parameter >> >> >> for >> >> >> the Parrinello-Rahman barostat. I tried to equilibrate my system >> >> using a >> >> >> Berendsen barostat before switching to Parrinello-Rahman for 1ns >> (and >> >> >> tau_p=1.0) but this didn´t help. Do you have any clue about where >> the >> >> >> problem originates from? >> >> >> >> >> >> >> >> >> Best >> >> >> >> >> >> Luther >> >> > >> >> > I guess this is a rounding issue in the box checking/correcting >> >> routines. >> >> > Could you change BOX_MARGIN in include/pbc.h from 0.5001 to 0.5005, >> >> > recompile gmxlib, mdlib and mdrun and see if the problem still >> occurs? >> >> > Please report back, so we can fix this for 3.3.3. >> >> > >> >> > Berk. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
