Re: [gmx-users] gromacs in parallel version
Looks like you are using MPICH2 as mpi software. Try including mpirun before mdrun_mpi. mpirun -n 4 mdun_mpi -v -s topol.tpr If that doesn't work you shoud run start the MPI DAEMON ( MPD ) before mpirun: mpdboot mpirun -n 2 mdun_mpi -v -s topol.tpr after you job finishes you might want to stop the mpi daemon by running: mpdallexit Diego. -- = Diego Enry B Gomes | PhD Student @ UFRJ - Brazil /tmp/home/@ Pacific Northwest National Laboratory Richland, WA. +1 (509) 372.6363 diegoenry.go...@pnl.gov = On Mar 6, 2009, at 5:13 AM, ANINDITA GAYEN wrote: Dear all, Sorry for the former post without any subject. I want to install gromacs in parallel version. I already have the normal version of gromacs and i want an MPI version of mdrun. The commands i have used are as followed. make distclean ./configure --enable-float --enable-mpi --prefix=/home/x --program- suffix=_mpi make mdrun -j 4 make install-mdrun [ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and in .bashrc include ... export CPPFLAGS=-I/home/x/fftw-3.2.1/include export LDFFLAGS=-L/home/x/fftw-3.2.1/lib] grmmacs installation run successfully. But when i run mdrun_mpi ..i got the message Can't read MPIRUN_MPD and the mdrun_mpi program does not run. Any suggestion regarding this problem will be highly acceptable. thanks in advance, Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now.___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] editconf and genbox using method
Hi, I want to obtain a dodecahedron box to start a simulation of a small peptide. But, even if I use dodecahedron option or octahedron, I obtain a rectangular box. Gromacs version: 4.0.4 compiled on redhat server 5 (I do this after 3.2.1 binaries for MS Windows) Command line that I used: pdb2gmx -f pep1.pdb -p pep1.top -o pep1.gro -water tip3p editconf -f pep1 -o -bt octahedron -d 0.3 -c genbox -cp out -cs -p pep1 -o pep1_em And, when I'm looking to pep1_em.gro with VMD the box is very very rectangular. Please, somebody help me with this problem. PS. I'm a new user of Gromacs but I'm read all the messages from the www.mail-archive.com/gmx-us...@*gromacs*.orghttp://www.mail-archive.com/gmx-users@gromacs.org about this problem but I still don't understand what I need to do to obtain the correct box. Thank you very much in advance for any suggestion. Marian ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] initial velocities Langevin dynamics
Hi there, I have a technical question, it might be silly but I couldn't find an answer so far. How are assigned the initial velocities for the particles when Langevin dynamics is performed? In normal MD the gen_vel/gen_seed are used for random generation of the initial velocities. I am used to vary this number with the same system in order to explore the effect of different initial conditions. I was wondering if there is such a possibility with Langevin dynamics, like changing the ld_seed number? thanks, loris... ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
- Original Message - From: Marian Butu marian.b...@gmail.com Date: Monday, March 9, 2009 21:24 Subject: [gmx-users] editconf and genbox using method To: gmx-users@gromacs.org editconf -f pep1 -o -bt octahedron -d 0.3 -c This command line should provoke some warnings at least. Have a look at them, and a read of editconf -h. Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options Nuno Azoia On Mon, 2009-03-09 at 12:23 +0200, Marian Butu wrote: Hi, I want to obtain a dodecahedron box to start a simulation of a small peptide. But, even if I use dodecahedron option or octahedron, I obtain a rectangular box. Gromacs version: 4.0.4 compiled on redhat server 5 (I do this after 3.2.1 binaries for MS Windows) Command line that I used: pdb2gmx -f pep1.pdb -p pep1.top -o pep1.gro -water tip3p editconf -f pep1 -o -bt octahedron -d 0.3 -c genbox -cp out -cs -p pep1 -o pep1_em And, when I'm looking to pep1_em.gro with VMD the box is very very rectangular. Please, somebody help me with this problem. PS. I'm a new user of Gromacs but I'm read all the messages from the www.mail-archive.com/gmx-users@gromacs.org about this problem but I still don't understand what I need to do to obtain the correct box. Thank you very much in advance for any suggestion. Marian ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
- Original Message - From: Nuno Azoia naz...@det.uminho.pt Date: Monday, March 9, 2009 21:52 Subject: Re: [gmx-users] editconf and genbox using method To: Discussion list for GROMACS users gmx-users@gromacs.org Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options I don't believe this is correct. That would be a bizarre thing for VMD to do. Much more likely is that editconf actually selected a rectangular box, genbox filled it, and VMD is displaying what's in the file. Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
Mark Abraham wrote: - Original Message - From: Nuno Azoia naz...@det.uminho.pt Date: Monday, March 9, 2009 21:52 Subject: Re: [gmx-users] editconf and genbox using method To: Discussion list for GROMACS users gmx-users@gromacs.org Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options I don't believe this is correct. That would be a bizarre thing for VMD to do. Much more likely is that editconf actually selected a rectangular box, genbox filled it, and VMD is displaying what's in the file. Actually, I've found trjconv to be necessary. VMD indeed shows a rectangular box for my dodecahedral systems, if I have not used trjconv -pbc mol -ur compact. The transformation to .pdb, however, is unnecessary. The .gro file can be processed in the same way. -Justin Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
Exactly. In my simulations with octahedron box I encounter the same problem. I just transform it in pdb to use it with pymol, that's all. But I have to use the same kind of options Justin use. Nuno Azoia On Mon, 2009-03-09 at 07:10 -0400, Justin A. Lemkul wrote: Mark Abraham wrote: - Original Message - From: Nuno Azoia naz...@det.uminho.pt Date: Monday, March 9, 2009 21:52 Subject: Re: [gmx-users] editconf and genbox using method To: Discussion list for GROMACS users gmx-users@gromacs.org Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options I don't believe this is correct. That would be a bizarre thing for VMD to do. Much more likely is that editconf actually selected a rectangular box, genbox filled it, and VMD is displaying what's in the file. Actually, I've found trjconv to be necessary. VMD indeed shows a rectangular box for my dodecahedral systems, if I have not used trjconv -pbc mol -ur compact. The transformation to .pdb, however, is unnecessary. The .gro file can be processed in the same way. -Justin Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Nuno Gonçalo Azoia Lopes Finishing Research Laboratory Textile Engineering Department Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
Thank you very much. Trjconv works fine. Marian On Mon, Mar 9, 2009 at 1:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: Mark Abraham wrote: - Original Message - From: Nuno Azoia naz...@det.uminho.pt Date: Monday, March 9, 2009 21:52 Subject: Re: [gmx-users] editconf and genbox using method To: Discussion list for GROMACS users gmx-users@gromacs.org Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options I don't believe this is correct. That would be a bizarre thing for VMD to do. Much more likely is that editconf actually selected a rectangular box, genbox filled it, and VMD is displaying what's in the file. Actually, I've found trjconv to be necessary. VMD indeed shows a rectangular box for my dodecahedral systems, if I have not used trjconv -pbc mol -ur compact. The transformation to .pdb, however, is unnecessary. The .gro file can be processed in the same way. -Justin Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] solvent temperature
Dear users I have the following problem and was wondering if anyone can help me. I'm trying to set up some SDS + water simulations, with Beredsen temperature coupling tcoupl = Berendsen tc-grps = system tau_t = 0.1 ref_t = 300 when I use the rigid solvent topology #include spc.itp and try to sample the system temperature with g_traj -f full -s full -ot temp.xvg -xvgr if I consider separately the temperature of the SDS and the Solvent, the SDS has the correct temperature (around 300 K), the solvent has a wrong temperature (around 200 K). The system as a whole has a wrong temperature (around 210 K). If I use the flexible solvent topology #include flexspc.itp then the temperature of the solvent is 300K, as expected. I have the same problem if I couple separately the SDS and the solvent to the termostat Tcoupl = Berendsen tc-grps = SDS SOL NA+ CL- tau_t = .1 .1 .1 .1 ref_t = 300 300 300 300 Did I do something wrong, or has this to do with the constraints in the SCP topology? Thank you in advance Alberto Imparato ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] solvent temperature
impar...@na.infn.it wrote: Dear users I have the following problem and was wondering if anyone can help me. I'm trying to set up some SDS + water simulations, with Beredsen temperature coupling tcoupl = Berendsen tc-grps = system tau_t = 0.1 ref_t = 300 when I use the rigid solvent topology #include spc.itp and try to sample the system temperature with g_traj -f full -s full -ot temp.xvg -xvgr if I consider separately the temperature of the SDS and the Solvent, the SDS has the correct temperature (around 300 K), the solvent has a wrong temperature (around 200 K). The system as a whole has a wrong temperature (around 210 K). Sounds like the exact same issue reported here: http://www.gromacs.org/pipermail/gmx-users/2002-August/002244.html Use g_energy to extract temperatures. If I use the flexible solvent topology #include flexspc.itp then the temperature of the solvent is 300K, as expected. I have the same problem if I couple separately the SDS and the solvent to the termostat Tcoupl = Berendsen tc-grps = SDS SOL NA+ CL- tau_t = .1 .1 .1 .1 ref_t = 300 300 300 300 Don't couple solvent and ions separately: http://wiki.gromacs.org/index.php/thermostats -Justin Did I do something wrong, or has this to do with the constraints in the SCP topology? Thank you in advance Alberto Imparato ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] The gromacs4 run err!
Hello everyone: When i do the tutor of gromacs4 in water, and input grompp -v,something wrong happen as below: This run will generate roughly 1 Mb of data writing run input file... There were 2 notes There was 1 warning --- Program grompp, VERSION 4.0.4 Source code file: gmx_fatal.c, line: 481 Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. --- Been There, Done It (Beavis and Butthead) Why do it show this err, how could I solve this problem? Thanks for everyone! javacfish ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The gromacs4 run err!
li bai wrote: Hello everyone: When i do the tutor of gromacs4 in water, and input grompp -v,something wrong happen as below: This run will generate roughly 1 Mb of data writing run input file... There were 2 notes There was 1 warning --- Program grompp, VERSION 4.0.4 Source code file: gmx_fatal.c, line: 481 Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. --- Been There, Done It (Beavis and Butthead) Why do it show this err, how could I solve this problem? The actual error message is printed as part of the grompp output. That is the issue you need to solve. Search the list archive and the wiki site, and post the actual error message if you still can't solve it. -Justin Thanks for everyone! javacfish 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/ ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question about parallel runing of gromacs
Hello, everyone: I have a question about mdrun_mpi, when I tried to run mdrun_mpi with two processors, the log file show everystep twice like the following, I am just wondering if that is normal. Thanks for help. Step=0, Dmax= 1.0e-02 nm, Epot= -2.08462e+06 Fmax= 1.93968e+04, atom= 82024 Step=0, Dmax= 1.0e-02 nm, Epot= -2.08462e+06 Fmax= 1.93968e+04, atom= 82024 Step=1, Dmax= 1.0e-02 nm, Epot= -2.20863e+06 Fmax= 8.61112e+03, atom= 61852 Step=1, Dmax= 1.0e-02 nm, Epot= -2.20863e+06 Fmax= 8.61112e+03, atom= 61852 Step=2, Dmax= 1.2e-02 nm, Epot= -2.32124e+06 Fmax= 5.29846e+03, atom= 149884 Step=2, Dmax= 1.2e-02 nm, Epot= -2.32124e+06 Fmax= 5.29846e+03, atom= 149884 .. best, mao ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Job Crash
Ilya Chorny wrote: I get the following and my job crashes. Is this just an i/o issue on my part? Any thoughts? Program mdrun_mpi, VERSION 4.0.3 Source code file: checkpoint.c, line: 859 File input/output error: Cannot rename checkpoint file; maybe you are out of quota? That seems pretty explicit to me. Check the file permissions and the available space on the file system. Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about parallel runing of gromacs
Xiang Mao wrote: Hello, everyone: I have a question about mdrun_mpi, when I tried to run mdrun_mpi with two processors, the log file show everystep twice like the following, I am just wondering if that is normal. Thanks for help. Step=0, Dmax= 1.0e-02 nm, Epot= -2.08462e+06 Fmax= 1.93968e+04, atom= 82024 Step=0, Dmax= 1.0e-02 nm, Epot= -2.08462e+06 Fmax= 1.93968e+04, atom= 82024 Step=1, Dmax= 1.0e-02 nm, Epot= -2.20863e+06 Fmax= 8.61112e+03, atom= 61852 Step=1, Dmax= 1.0e-02 nm, Epot= -2.20863e+06 Fmax= 8.61112e+03, atom= 61852 Step=2, Dmax= 1.2e-02 nm, Epot= -2.32124e+06 Fmax= 5.29846e+03, atom= 149884 Step=2, Dmax= 1.2e-02 nm, Epot= -2.32124e+06 Fmax= 5.29846e+03, atom= 149884 .. I suspect you're running two single-processor calculations, but since you haven't told us your command line, we can only guess. Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about parallel runing of gromacs
My PC has a intel core2 cpu. I compiled gromacs under cygwin, and using MPICH2. After mpiboot, I use mpirun -n 2 mdrun_mpi to run EM, MD. thanks. mao On Mon, Mar 9, 2009 at 11:56 AM, Mark Abraham mark.abra...@anu.edu.auwrote: Xiang Mao wrote: Hello, everyone: I have a question about mdrun_mpi, when I tried to run mdrun_mpi with two processors, the log file show everystep twice like the following, I am just wondering if that is normal. Thanks for help. Step=0, Dmax= 1.0e-02 nm, Epot= -2.08462e+06 Fmax= 1.93968e+04, atom= 82024 Step=0, Dmax= 1.0e-02 nm, Epot= -2.08462e+06 Fmax= 1.93968e+04, atom= 82024 Step=1, Dmax= 1.0e-02 nm, Epot= -2.20863e+06 Fmax= 8.61112e+03, atom= 61852 Step=1, Dmax= 1.0e-02 nm, Epot= -2.20863e+06 Fmax= 8.61112e+03, atom= 61852 Step=2, Dmax= 1.2e-02 nm, Epot= -2.32124e+06 Fmax= 5.29846e+03, atom= 149884 Step=2, Dmax= 1.2e-02 nm, Epot= -2.32124e+06 Fmax= 5.29846e+03, atom= 149884 .. I suspect you're running two single-processor calculations, but since you haven't told us your command line, we can only guess. Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Job Crash
Yeah it was a permission error. It confused me because it happened mid stream. Sorry for wasting people time. ::) Thanks, Ilya On Mon, Mar 9, 2009 at 9:55 AM, Mark Abraham mark.abra...@anu.edu.auwrote: Ilya Chorny wrote: I get the following and my job crashes. Is this just an i/o issue on my part? Any thoughts? Program mdrun_mpi, VERSION 4.0.3 Source code file: checkpoint.c, line: 859 File input/output error: Cannot rename checkpoint file; maybe you are out of quota? That seems pretty explicit to me. Check the file permissions and the available space on the file system. Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 58
I've used this tutorial: https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf I've used command line: editconf -c -f conf.gro -bt dodecahedron -d 0.7 -o box.gro to center the protein, but the problem remains - protein is still in the edge of the water box. There is also 1-4 warning for which I see no reasons and very fast presision reached time. Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 200 Warning: 1-4 interaction between 2 and 21 at distance 6.197 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step= 14, Dmax= 1.2e-06 nm, Epot= 2.82932e+24 Fmax= inf, atom= 4 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 2.8293175e+24 Maximum force =inf on atom 4 Norm of force =inf gcq#239: killing children ... (Insight/Parasoft) and...@linux-f29d:~/GROMACS_MD/FZD1 Here are MDP files: EM.mdp integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 nstenergy = 10 constraints = none integrator = md nsteps = 2500 dt = 0.002 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 Pcoupl = Berendsen tau-p = 1.0 compressibility = 5e-5 5e-5 5e-5 0 0 0 ref-p = 1.0 nstenergy = 100 define = -DPOSRES Best regards, Andrew -- Message: 3 Date: Fri, 06 Mar 2009 13:41:28 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] .gro files problems To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 49b16e58.3000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Andrew Voronkov wrote: Dear GROMACS users, I'm trying to do this tutorial It's always best to post a link to the tutorial you're using. There are dozens of Gromacs tutorials out there. with 1ijy structure from rcsb.org All .gro files on different step raise questions. 1) conf.gro - by VMD I see some strange groups which are not linked with the protein. This may or may not be an artefact of VMD's efforts to guess where bonds should be. Sometimes it's smart, sometimes it's not. 2) After solvatation step in solvated.gro the protein is not in the middle of solution but somewhere in the edge, how to solve this? editconf -c 3) After energy minimization protein even goes out of the solution. Looks like I am doing everything according to the tutorial (except the structure) but there are still problems... Use editconf -c and try again. The .gro files are in the attachment. The listserv ate them, but they probably won't aid much in diagnosis, anyway. On minimization step I also get: Steepest Descents converged to machine precision in 73 steps, but did not reach the requested Fmax Depending on what your target Fmax was, this may not be a problem. Fmax 1000 is generally adequate for a simple protein in water. On equilibration step I also get an error(with such .gro file it very proabable): Or you could have an error in your .mdp file (inappropriate parameters, etc), so if things continue to fail, post the .mdp file (not as an attachment, just embed the text). -Justin ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gmx-users Digest, Vol 59, Issue 58
Yes I read somewhere that treating the simulation space as a cube has some drawbacks. I'll try these parameters. On Mon, Mar 9, 2009 at 3:36 PM, Andrew Voronkov drugdes...@yandex.ru wrote: I've used this tutorial: https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf I've used command line: editconf -c -f conf.gro -bt dodecahedron -d 0.7 -o box.gro to center the protein, but the problem remains - protein is still in the edge of the water box. There is also 1-4 warning for which I see no reasons and very fast presision reached time. Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps = 200 Warning: 1-4 interaction between 2 and 21 at distance 6.197 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step= 14, Dmax= 1.2e-06 nm, Epot= 2.82932e+24 Fmax= inf, atom= 4 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 2.8293175e+24 Maximum force = inf on atom 4 Norm of force = inf gcq#239: killing children ... (Insight/Parasoft) and...@linux-f29d:~/GROMACS_MD/FZD1 Here are MDP files: EM.mdp integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 nstenergy = 10 constraints = none integrator = md nsteps = 2500 dt = 0.002 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 Pcoupl = Berendsen tau-p = 1.0 compressibility = 5e-5 5e-5 5e-5 0 0 0 ref-p = 1.0 nstenergy = 100 define = -DPOSRES Best regards, Andrew -- Message: 3 Date: Fri, 06 Mar 2009 13:41:28 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] .gro files problems To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 49b16e58.3000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Andrew Voronkov wrote: Dear GROMACS users, I'm trying to do this tutorial It's always best to post a link to the tutorial you're using. There are dozens of Gromacs tutorials out there. with 1ijy structure from rcsb.org All .gro files on different step raise questions. 1) conf.gro - by VMD I see some strange groups which are not linked with the protein. This may or may not be an artefact of VMD's efforts to guess where bonds should be. Sometimes it's smart, sometimes it's not. 2) After solvatation step in solvated.gro the protein is not in the middle of solution but somewhere in the edge, how to solve this? editconf -c 3) After energy minimization protein even goes out of the solution. Looks like I am doing everything according to the tutorial (except the structure) but there are still problems... Use editconf -c and try again. The .gro files are in the attachment. The listserv ate them, but they probably won't aid much in diagnosis, anyway. On minimization step I also get: Steepest Descents converged to machine precision in 73 steps, but did not reach the requested Fmax Depending on what your target Fmax was, this may not be a problem. Fmax 1000 is generally adequate for a simple protein in water. On equilibration step I also get an error(with such .gro file it very proabable): Or you could have an error in your .mdp file (inappropriate parameters, etc), so if things continue to fail, post the .mdp file (not as an attachment, just embed the text). -Justin ___ gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-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
SV: SV: [gmx-users] g_order version 4.0.x
Dear Justin and others, I have now tried the exact same command g_order command with the exact same result: /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 This gives - again - the wanted file for the deuterium order parameters, dmpclim3_order_4.xvg, and also the non-requested for file order.xvg. Both files - again - contain no parameters: /data1/PROJECTS/LIMONENE/LIM-BILAYERS/DMPC/3 more dmpclim3_order_4.xvg # This file was created Mon Mar 9 21:45:17 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 # # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title Deuterium order parameters @xaxis label Atom @yaxis label Scd @TYPE xy /data1/PROJECTS/LIMONENE/LIM-BILAYERS/DMPC/3 more order.xvg # This file was created Mon Mar 9 21:45:17 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 # # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title Order tensor diagonal elements @xaxis label Atom @yaxis label S @TYPE xy This is driving me crazy. Clearly I must be doing something wrong since it is working for Justin - but what? If anyone has any suggestions they'll be much appreciated! Another thing: David van der Spoel asked me to file a bugzilla which I have done. After the email from Justin he wrote to me and asked whether version 4.0.4 was working for me. I wanted to write him back to answer him that I would try this today when I was back from holiday, but every time I tried to email him my email couldn't be delivered. Am I - again - doing something wrong, or do I have bad gromacs karma? Best regards and thank you, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Sarah Witzke Sendt: ti 03-03-2009 11:37 Til: jalem...@vt.edu; Discussion list for GROMACS users Emne: SV: SV: [gmx-users] g_order version 4.0.x Good idea, I'll try that when I get home next week. -Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: ma 02-03-2009 13:58 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Thank you David, I have filled a bugzilla. g_order works for me under version 4.0.4, perhaps try an upgrade? -Justin Fra: gmx-users-boun...@gromacs.org på vegne af David van der Spoel Sendt: ma 02-03-2009 10:55 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Dear Gromacs users, I'm sorry to resend this email but I sent it yesterday (27 hours ago) and I still haven't received it myself. I'm sorry for the inconvenience it might cause. Sarah Dear Gromacs Users, I have simulated a lipid bilayer (128 DMPC molecules) with some small hydrophobic molecules. These small molecules go from the water into the bilayer and I now want to do some analysis to see, whether this has changed e.g. membrane thickness or the order of the lipid tails. I'm new to gromacs and this is my first try with analysis. For analysing the order of the lipid tales, I use g_order. The first index file I created consisted of 28 groups - one for each of the 14 carbons (including the carbonyl-C) in the two chains. The atoms in each of the 128 lipid molecules have the same atom name (e.g. c1, c2...) so each of the 28 groups in the index file consist of 128 atoms (an entry in make_ndx would look like this a c15 r DMPC). Then I tried g_order version 4.0.2: g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_2.xvg I'm asked to Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation: and then all the 28 groups are listed. This was not what I had expected; I thought g_order calculated the order parameter for all the tail carbons at once. I tried just choosing group 0 to see what happened: Not much - as was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg. This I found strange since I hadn't asked for them, but then I found this bugzilla report: http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ (no. 264) After reading that I also tried to specify all carbons
Re: SV: SV: [gmx-users] g_order version 4.0.x
Sarah Witzke wrote: Dear Justin and others, I have now tried the exact same command g_order command with the exact same result: /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 How long is the trajectory? Does the command work if you don't use -b? Maybe a huge skip in time is causing problems, although I don't think it should. What is in your .ndx file? This gives - again - the wanted file for the deuterium order parameters, dmpclim3_order_4.xvg, and also the non-requested for file order.xvg. Right, order.xvg is generated by default, whether you specify it or not. -Justin Both files - again - contain no parameters: /data1/PROJECTS/LIMONENE/LIM-BILAYERS/DMPC/3 more dmpclim3_order_4.xvg # This file was created Mon Mar 9 21:45:17 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 # # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title Deuterium order parameters @xaxis label Atom @yaxis label Scd @TYPE xy /data1/PROJECTS/LIMONENE/LIM-BILAYERS/DMPC/3 more order.xvg # This file was created Mon Mar 9 21:45:17 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 # # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title Order tensor diagonal elements @xaxis label Atom @yaxis label S @TYPE xy This is driving me crazy. Clearly I must be doing something wrong since it is working for Justin - but what? If anyone has any suggestions they'll be much appreciated! Another thing: David van der Spoel asked me to file a bugzilla which I have done. After the email from Justin he wrote to me and asked whether version 4.0.4 was working for me. I wanted to write him back to answer him that I would try this today when I was back from holiday, but every time I tried to email him my email couldn't be delivered. Am I - again - doing something wrong, or do I have bad gromacs karma? Best regards and thank you, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Sarah Witzke Sendt: ti 03-03-2009 11:37 Til: jalem...@vt.edu; Discussion list for GROMACS users Emne: SV: SV: [gmx-users] g_order version 4.0.x Good idea, I'll try that when I get home next week. -Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: ma 02-03-2009 13:58 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Thank you David, I have filled a bugzilla. g_order works for me under version 4.0.4, perhaps try an upgrade? -Justin Fra: gmx-users-boun...@gromacs.org på vegne af David van der Spoel Sendt: ma 02-03-2009 10:55 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Dear Gromacs users, I'm sorry to resend this email but I sent it yesterday (27 hours ago) and I still haven't received it myself. I'm sorry for the inconvenience it might cause. Sarah Dear Gromacs Users, I have simulated a lipid bilayer (128 DMPC molecules) with some small hydrophobic molecules. These small molecules go from the water into the bilayer and I now want to do some analysis to see, whether this has changed e.g. membrane thickness or the order of the lipid tails. I'm new to gromacs and this is my first try with analysis. For analysing the order of the lipid tales, I use g_order. The first index file I created consisted of 28 groups - one for each of the 14 carbons (including the carbonyl-C) in the two chains. The atoms in each of the 128 lipid molecules have the same atom name (e.g. c1, c2...) so each of the 28 groups in the index file consist of 128 atoms (an entry in make_ndx would look like this a c15 r DMPC). Then I tried g_order version 4.0.2: g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_2.xvg I'm asked to Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation: and then all the 28 groups are listed. This was not what I had expected; I thought g_order calculated the order parameter for all the tail carbons at once. I tried just choosing group 0 to see what happened: Not much - as was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg. This I found strange since I hadn't asked for them, but then I found this
SV: SV: SV: [gmx-users] g_order version 4.0.x
My .xtc file is 219.41 ns and therefor I thought to just use the last ~100 ns where my molecules have diffused into the membrane. I have just run g_order again whitout the -b option: the result is the same, no order parameters. My index file consists of just one big group. In that groups are the carbon atoms of the two lipid chains (and the two carbonyl carbons) for each of my 128 lipids. When running g_order it reads the .ndx file like this: /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_5.xvg :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 4.0.4 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order (-: Option Filename Type Description -f dmpclim3-all.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -n dmpc_order.ndx InputIndex file -s dmpclim3-1.tpr InputRun input file: tpr tpb tpa -o order.xvg Output xvgr/xmgr file -od dmpclim3_order_5.xvg Output xvgr/xmgr file -os sliced.xvg Output xvgr/xmgr file -Sg sg-ang.xvg Output, Opt. xvgr/xmgr file -Sksk-dist.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -d enum z Direction of the normal on the membrane: z, x or y -sl int1 Calculate order parameter as function of boxlength, dividing the box in #nr slices. -[no]szonly bool no Only give Sz element of order tensor. (axis can be specified with -d) -[no]unsat bool no Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. Taking z axis as normal to the membrane Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Using following groups: Groupname: C15__DMPC_C17__DMPC_C18__DMPC_C19__DMPC_C20__DMPC_C21__DMPC_C22__DMPC_C23__DMPC_C24__DMPC_C25__DMPC_C26__DMPC_C27__DMPC_C28__DMPC_C29__DMPC_C32__DMPC_C34__DMPC_C35__DMPC_C36__DMPC_C37__DMPC_C38__DMPC_C39__DMPC_C40__DMPC_C41__DMPC_C42__DMPC_C43__DMPC_C44__DMPC_C45__DMPC_C46__DMPC First atomname: C15 First atomnr 44 Reading frame 0 time0.000 Number of elements in first group: 3584 Reading frame 21000 time 21.016 Read trajectory. Printing parameters to file Back Off! I just backed up order.xvg to ./#order.xvg.3# Thank you for your very quick reply! Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: ma 09-03-2009 22:38 Til: Discussion list for GROMACS users Emne: Re: SV: SV: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Dear Justin and others, I have now tried the exact same command g_order command with the exact same result: /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 How long is the trajectory? Does the command work if you don't use -b? Maybe a huge skip in time is causing problems, although I don't think it should. What is in your .ndx file? This gives - again - the wanted file for the deuterium order parameters, dmpclim3_order_4.xvg, and also the non-requested for file order.xvg. Right, order.xvg is generated by default, whether you specify it or not. -Justin Both files - again - contain no parameters: /data1/PROJECTS/LIMONENE/LIM-BILAYERS/DMPC/3 more dmpclim3_order_4.xvg # This file was created Mon Mar 9 21:45:17 2009 # by the following command: #
Re: [gmx-users] genion command with PDB files for amber03 force field
Hi, To set things straight a bit. If you are using ion-related GROMACS tools, such as genion, you will need to enter the AMBER ion definition to the ions.itp file in the top directory of the GROMACS distribution. This isn't too tough, as all the parameters for the ions are included with the Amber ports, but genion needs them to be in the ions.itp (or other suitable) file. This has nothing to do with genion. Genion just uses the names for ions that are given (either explicitly or as default) with options -pname and -nname. When the ions occur in the system (under [ system ] in the .top file), they have to be defined somewhere as moleculetypes. Otherwise grompp will complain; no other program. ions.itp is just an intuitive place for these moleculetype definitions. Please inform yourself well regarding the way gromacs handles topologies. Check chapter 5 of the manual. This goes double when answering posts on such topics. Although such efforts are commonly appreciated, (partly) wrong information may send the original poster further off. Dear gromacs users, I am using genion command to add ions to .tpr file which was made for protein by use of amber03 force field. In intial pdb file N-terminal amino acid is NHIE, but genion changes it to NHI, which isnot recognized by next pdb2gmx. This is not a big problem , but it looks is a little bit like a bug. Justin answered this part of the question. For a suitable scheme to set up your simulations, you may want to check http://www.nmr.chem.uu.nl/~tsjerk/course/molmod/md.html 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 listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: SV: SV: SV: [gmx-users] g_order version 4.0.x
Sarah Witzke wrote: My .xtc file is 219.41 ns and therefor I thought to just use the last ~100 ns where my molecules have diffused into the membrane. I have just run g_order again whitout the -b option: the result is the same, no order parameters. My index file consists of just one big group. In that groups are the carbon atoms of the two lipid chains (and the two carbonyl carbons) for each of my 128 lipids. When running g_order it reads the .ndx file like this: That is your problem. You need individual groups for each distinct carbon along the chain. For an example for proper creation of these groups, see here: http://wiki.gromacs.org/index.php/make_ndx -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: SV: SV: SV: [gmx-users] g_order version 4.0.x
Justin A. Lemkul wrote: Sarah Witzke wrote: My .xtc file is 219.41 ns and therefor I thought to just use the last ~100 ns where my molecules have diffused into the membrane. I have just run g_order again whitout the -b option: the result is the same, no order parameters. My index file consists of just one big group. In that groups are the carbon atoms of the two lipid chains (and the two carbonyl carbons) for each of my 128 lipids. When running g_order it reads the .ndx file like this: That is your problem. You need individual groups for each distinct carbon along the chain. For an example for proper creation of these groups, see here: http://wiki.gromacs.org/index.php/make_ndx *Edit* I have gone ahead and created a g_order page. The information about how to create index groups seems to fit better there. Please refer to the new g_order page: http://wiki.gromacs.org/index.php/g_order -Justin -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about parallel runing of gromacs
Xiang Mao wrote: My PC has a intel core2 cpu. I compiled gromacs under cygwin, and using MPICH2. After mpiboot, I use mpirun -n 2 mdrun_mpi to run EM, MD. OK that might be working right. Now you need to look in the log file for an indication of whether the run has two component processes or one - right at the top, usually. Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb2gmx -vsite h hangs
Hi I am running 4.0.3. I wanted to test the 4fs timestep with virtual sites. I will be running a simulation with ~500K atoms. I created a water box with ~500K atoms. I then type pdb2gmx -f water.gro -o water_vsite.gro -vsite h -p topol I get the following output at which point it hangs. I waited for about 2 hrs before killing it. Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/elements.dat Entries in elements.dat: 218 Reading water_solv.gro... Read '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 587676 atoms Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 0 chains and 1 blocks of water and 195892 residues with 587676 atoms chain #res #atoms 1 '-' 195892 587676 (only water) No occupancies in water_solv.gro Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp Residue 56 Sorting it all out... Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.hdb Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-n.tdb Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 (587676 atoms, 195892 residues) There are 195892 donors and 195892 acceptors There are 280210 hydrogen bonds Checking for duplicate atoms Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/specbond.dat 7 out of 7 lines of specbond.dat converted succesfully Thanks, Ilya -- Ilya Chorny Ph.D. -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx -vsite h hangs
Ilya Chorny wrote: Hi I am running 4.0.3. I wanted to test the 4fs timestep with virtual sites. I will be running a simulation with ~500K atoms. At least your GMXLIB environment variable is pointing to a CVS version of 4.0.4 (if you named that correctly). If you're having trouble, make sure you have a clean install of a known and preferably most-recent version. The wiki has a page on the correct use of GMXRC to make sure of such things. Mark ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx -vsite h hangs
Ilya Chorny wrote: Hi I am running 4.0.3. I wanted to test the 4fs timestep with virtual sites. I will be running a simulation with ~500K atoms. From the manual, section 6.5: For the hydrogens in water and in hydroxyl, sulfhydryl or amine groups, no degrees of freedom can be removed, because rotational freedom should be preserved. The only other option available to slow down these motions, is to increase the mass of the hydrogen atoms at the expense of the mass of the connected heavy atom. Try pdb2gmx -heavyh. When diagnosing a problem, make it simple. Processing 500,000 atoms may indeed take a long time. If you create a test case with a single water molecule and write the topology, pdb2gmx actually completes successfully, however, per the quote above, no virtual sites are generated. -Justin I created a water box with ~500K atoms. I then type pdb2gmx -f water.gro -o water_vsite.gro -vsite h -p topol I get the following output at which point it hangs. I waited for about 2 hrs before killing it. Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/elements.dat Entries in elements.dat: 218 Reading water_solv.gro... Read '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 587676 atoms Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 0 chains and 1 blocks of water and 195892 residues with 587676 atoms chain #res #atoms 1 '-' 195892 587676 (only water) No occupancies in water_solv.gro Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp Residue 56 Sorting it all out... Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.hdb Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-n.tdb Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 (587676 atoms, 195892 residues) There are 195892 donors and 195892 acceptors There are 280210 hydrogen bonds Checking for duplicate atoms Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/specbond.dat 7 out of 7 lines of specbond.dat converted succesfully Thanks, Ilya -- Ilya Chorny Ph.D. -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx -vsite h hangs
Justin, Thanks for pointing me to section 6.5. I am running ~500K atoms because I want to test the scaling as well. So I'm confused. How can I use pdb2gmx -vsite h this to run a protein and water simulation with a 4fs timestep as described in the Gromacs 4.0 paper if -vsite does not apply to OH/NH hydrogens. They don't describe using heavyh in the paper and there are earlier posts that teach away from using heavyh. Thanks, Ilya On Mon, Mar 9, 2009 at 7:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ilya Chorny wrote: Hi I am running 4.0.3. I wanted to test the 4fs timestep with virtual sites. I will be running a simulation with ~500K atoms. From the manual, section 6.5: For the hydrogens in water and in hydroxyl, sulfhydryl or amine groups, no degrees of freedom can be removed, because rotational freedom should be preserved. The only other option available to slow down these motions, is to increase the mass of the hydrogen atoms at the expense of the mass of the connected heavy atom. Try pdb2gmx -heavyh. When diagnosing a problem, make it simple. Processing 500,000 atoms may indeed take a long time. If you create a test case with a single water molecule and write the topology, pdb2gmx actually completes successfully, however, per the quote above, no virtual sites are generated. -Justin I created a water box with ~500K atoms. I then type pdb2gmx -f water.gro -o water_vsite.gro -vsite h -p topol I get the following output at which point it hangs. I waited for about 2 hrs before killing it. Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/elements.dat Entries in elements.dat: 218 Reading water_solv.gro... Read '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 587676 atoms Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 0 chains and 1 blocks of water and 195892 residues with 587676 atoms chain #res #atoms 1 '-' 195892 587676 (only water) No occupancies in water_solv.gro Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.rtp Residue 56 Sorting it all out... Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa.hdb Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-n.tdb Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 (587676 atoms, 195892 residues) There are 195892 donors and 195892 acceptors There are 280210 hydrogen bonds Checking for duplicate atoms Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/specbond.dat 7 out of 7 lines of specbond.dat converted succesfully Thanks, Ilya -- Ilya Chorny Ph.D. -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search
Re: [gmx-users] question about parallel runing of gromacs
On Mar 9, 2009, at 5:12 PM, Mark Abraham wrote: Xiang Mao wrote: My PC has a intel core2 cpu. I compiled gromacs under cygwin, and using MPICH2. After mpiboot, I use mpirun -n 2 mdrun_mpi to run EM, MD. OK that might be working right. Now you need to look in the log file for an indication of whether the run has two component processes or one - right at the top, usually. Mark Hi Xiang, maybe the solution is simple and you just didn't use the -- enable-mpi flag in the ./configure step. That explains the duplicate steps. Try a quick ldd test to check if MPI compilation worked. % which mdrun_mpi (find where mdrun was installed, mine is at /usr/ local/gmx4/bin/) % ldd /usr/local/gmx4/bin/mdrun_mpi You should see libmpi.so.0 in the list of libraries, if not, go back to the ./configure step. Diego -- = Diego Enry B Gomes | PhD Student @ UFRJ - Brazil /tmp/home/@ Pacific Northwest National Laboratory Richland, WA. +1 (509) 372.6363 diegoenry.go...@pnl.gov =___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in pdb file after SA
Hi all I have done MD job on a 226 residue protein with cubic box -d 0.9 in the editconf step. after 30 ns I entered the last step pdb to the simulating annealing, again with cubic box and -d 0.9. the highest temp was 600 K and the loest was 50 K. When I see the pdb of structures at 300 K, 600 K and 50 K in pymol, it seems the structures converts to 2 part, one along oneside of cubic's surface the other was in the parallel side, I mean that the system move out of the cubic, and the outer part appears in another side of cubic, so I dont have the integrate structure. How can I fix this problem. Thank you in advance for your help. -- Tehran University of Medical Sciences www.tums.ac.ir -- 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 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
