Hi Tsjerk, Thanks. I will try that. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, May 16, 2007 4:41 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PBC problem Hi Yuguang, Gromacs should automatically fix the box to meet the requirements during an mdrun with pressure coupling (but does sometimes fail). There is also a certain tolerance in gromacs for the deviations. Anyway.., you can download a version of GMX3.2.1 from http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.2.1-rtc.tgz in which I modified editconf.c (and pbc.c/pbc.h) to have an option for changing any triclinic box into a box which conforms to the gromacs rules. Maybe you just want to get the parts of the code involved and transfer them to GMX3.3.1, which should be quite straightforward. The developers are welcome to incorporate the option/code if they like to include it. The editconf option I added is -fix. Note that editconf will still issue a warning about the skewness of the box, but on a 'fixed' structure, that should not occur anymore. Hope it helps, Tsjerk On 5/16/07, Mu Yuguang (Dr) <[EMAIL PROTECTED]> wrote: > Thanks Tsjerk, > Probably because we use pressure coupling and the box size is deformed. > > Best regards > Yuguang > > Dr. Yuguang Mu > Assistant Professor > School of Biological Sciences > Nanyang Technological University > 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 > http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php > > > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar > Sent: Wednesday, May 16, 2007 12:49 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] PBC problem > > Hi Yuguang, > > > Warning: Triclinic box is too skewed. > > Box (3x3): > > Box[ 0]={ 6.46530e+00, 0.00000e+00, 0.00000e+00} > > Box[ 1]={ 2.14552e+00, 6.10274e+00, 0.00000e+00} > > Box[ 2]={-2.14464e+00, 3.05200e+00, 5.24664e+00} > > This is not a rhombic dodecahedron. > > > CRYST1 64.653 64.689 64.375 70.32 109.46 70.63 P 1 1 > > This shows that the second vector is larger than the first, thus > violating the gromacs rules for proper boxes (manual chapter 3; > although it could be handled a bit more liberally, especially in the > analysis tools). > > Cheers, > > Tsjerk > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
