[gmx-users] Re: New version of dock.pl (Cesar Araujo)
Link is not working.. -- == Dr. JORGE HERNANDEZ FERNANDEZ == == Center of Applied Toxinology == = CAT-CEPID - Instituto Butantan = == Ave Vital Brasil, 1500 S.P. == Tel: 055 11 3726 7222 r.2042 Fax: 055 11 3721 6605 S.B.I.- EMBRAPA - BioInformatica C.p. 6041 Cidade Universitária "Zeferino Vaz" = Barão Geraldo Campinas S.P. === 13080-970 Tel: 055 19-37895828 Cell: 055 11-97126104 The information contained in this e-mail and any files tr > Date: Wed, 18 Oct 2006 13:16:26 -0700 > From: "Cesar Araujo" <[EMAIL PROTECTED]> > Subject: [gmx-users] New version of dock.pl > To: > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi everybody, > > I've submitted a new version of my script dock.pl. You can find the > new version in the contributed software of the Gromacs website. This > version fix some bugs and add new functionality like growing the > ligand at the binding site of a protein. Please, read the > documentation for more details about the new features. > > By the way, I haven't received any feedback about this script. So, > if you are a user, I would appreciate if you can send me any > comments about it. > > Thanks in advance, > > César.- > > --- > Cesar Araujo, Lic. of Chemistry > Research Center for Molecular Endocrinology > P.O. Box 5000, FIN-90014 University of Oulu > Finland > > phone: +358 8 3155632 > e-mail: [EMAIL PROTECTED] > -- next part -- > An HTML attachment was scrubbed... > URL: http://www.gromacs.org/pipermail/gmx- > users/attachments/20061018/f3b32605/attachment-0001.html > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Paralell problems...
Dear GRMxers: We need some help in running our Gromacs 3.2.1 parallel environment in 5 nodes of SunFires V20v (dual-core Opteron 2.2, 4 GB DDR2 RAM), gigabit eth, mpich-1.2.7, using Sun Grid Engine 6.0. In a 2 processors job (single node), the results are O.K. but in a 4, 6 or 8 processors (2, 3 or 4 nodes) in the machine log files we have: In “ -np 4” the error was : p4_5991: p4_error: Timeout in establishing connection to remote process: 0 p0_8456: p4_error: net_recv read: probable EOF on socket: 1 p5_5996: p4_error: Timeout in establishing connection to remote process: 0 p0_8456: (333.761719) net_send: could not write to fd=4, errno = 32 In “ –np 8” the error was: p0_16398: p4_error: interrupt SIGSEGV: 11 In all the cases, we obtain a “Killed by signal 2” at the end of the gromacs log, and process stopped. Grompp was executed with the -np option, and our final script was: #$ -v MPIRUN #$ -v MPICH_PROCESS_GROUP MPIRUN -np $NSLOTS -machinefile $TMPDIR/machinefile /nfs/gromacs-3.2. 1_paralelo/x86_64-unknown-linux-gnu/bin/mdrun -np 6 -s ABint/ABint_md.tpr -o ABint/ABint_md.trr -c ABint/ABint_md.gro -e ABint/ABintener.edr -g ABint/ ABintmd.log -nice 0 Any help will be extremely appreciated: Jorge H.F. -- == Dr. JORGE HERNANDEZ FERNANDEZ == == Center of Applied Toxinology == = CAT-CEPID - Instituto Butantan = == Ave Vital Brasil, 1500 S.P. == Tel: 055 11 3726 7222 r.2042 Fax: 055 11 3721 6605 S.B.I.- EMBRAPA - BioInformatica C.p. 6041 Cidade Universitária "Zeferino Vaz" = Barão Geraldo Campinas S.P. === 13080-970 Tel: 055 19-37895828 Cell: 055 11-97126104 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
