Hi Berk, thanks for your advice! I will try what you suggested and report back when I have got the results.
Luther >> Date: Mon, 28 Jan 2008 15:29:28 +0100 >> From: [EMAIL PROTECTED] >> To: [email protected] >> Subject: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling >> 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
