[gmx-users] Can gromacs automatically divided trajectory file into several parts during the simulation process?
Dear all, I am now try to do a long-time all atom simulation. The trajectory file is expected to be larger than 20G bytes. However, my simulation is run on a cluster which only allows me to store 5G bytes file. Therefore, I attempt to divided the trajectory file into several parts but not interrupt the simulation. Does anyone know how to do? Many thanks! Justin Zhang -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] P4_error for extending coarse grained MD simulations
Hi Carsten, The error message I post is got on a single core with MPI. p0_6991: p4_error: interrupt SIGSEGV: 11 So it states p0_. I dont think the error is due to the MPI progrom. Am I right? Justin Zhang 在 2010年7月9日 下午4:00，Carsten Kutzner 写道： > Hi Justin, > > what kind of error message do you get if you run this system > on a single core without MPI? > > Carsten > > > On Jul 8, 2010, at 9:36 PM, 张春雷 wrote: > > Dear all, > > I have post this question about a two weeks ago. During these days, I > followed suggestions from Mark and weixin, but did not fix it. Here, I > repeat it again to seek more help. > > I attempt to extend MD simulation for a coarse-grained system. CG models > are in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or > 4.07. > > I tried to use check point file state.cpt to extend my simulation. The > mdrun program can read to the check file. But it reported error like this: > > Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 > > Loaded with Money > > starting mdrun 'Protein in POPE bilayer' > 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). > step 1200, remaining runtime: 0 s > p0_6991: p4_error: interrupt SIGSEGV: 11 > > I check the *state.cpt* file using *gmxdump* and compare it with other > checkpoint files that can be used for extending All-atom simulations. I > found that in the CG check point file, some sections are missing: *box-v > (3x3)* and *thermostat-integral*. > I am not sure whether this missing sections cause my run crash. If it is, > could any one tell me possible reasons that result in the loss of box-v and > thermostat-integral and how to fix the problem? > > Your suggestions are greatly helpful and appreciated. > > Justin Zhang > > > > 在 2010年6月25日 下午4:45，张春雷 写道： > >> Information shown by gmxcheck: >> >> *Checking file state.cpt* >> >> # Atoms 9817 >> Last frame -1 time 36.000 >> >> >> Item#frames Timestep (ps) >> Step 1 >> Time 1 >> Lambda 1 >> Coords 1 >> Velocities 1 >> Forces 0 >> Box 1 >> >> *Checking file state_prev.cpt* >> >> # Atoms 9817 >> Last frame -1 time 359010.000 >> >> >> Item#frames Timestep (ps) >> Step 1 >> Time 1 >> Lambda 1 >> Coords 1 >> Velocities 1 >> Forces 0 >> Box 1 >> >> *Checking file md_360ns.trr* >> trn version: GMX_trn_file (double precision) >> Reading frame 0 time0.000 >> # Atoms 9817 >> Reading frame 2000 time 30.000 >> >> >> Item#frames Timestep (ps) >> Step 2401150 >> Time 2401150 >> Lambda2401150 >> Coords2401150 >> Velocities2401150 >> Forces 0 >> Box 2401150 >> >> Is anything wrong? >> >> >> 2010/6/25 Mark Abraham >> >> >>> >>> - Original Message - >>> From: 张春雷 >>> Date: Friday, June 25, 2010 16:46 >>> Subject: Re: [gmx-users] P4_error for extending coarse grained MD >>> simulations >>> To: Discussion list for GROMACS users >>> >>> > The last .gro file only provides coordinates of the system. No >>> velocity is recorded. Actually, what I attempt to achieve is a binary >>> identical trajectory. So I think the velocity from the last step is >>> critical. >>> > >>> > I have tried another approach in which the checkpoint file is >>> neglected. >>> > >>> > $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g >>> md_720ns.log >>> > >>> > It works. So the checkpoint file appears to contain some error. But it >>> is generated by a normally finished production simulation. >>> >>> What does gmxcheck say about all the files involved? >>> >>> Mark >>> >>> >>> > Have you encountered similar things? >>> > >>> > Thank you for your suggestions! >>> > >>> > >>> > >>> > 在 2010年6月25日 上午9:16，weixin 写道： >>> >>>> > >>>> > How about using the last .gro file to continue your simulation? >>>> > >>>> > >>>> > >>>> > 2010/6/24 张春雷 >>>> >>
Re: [gmx-users] P4_error for extending coarse grained MD simulations
Dear all, I have post this question about a two weeks ago. During these days, I followed suggestions from Mark and weixin, but did not fix it. Here, I repeat it again to seek more help. I attempt to extend MD simulation for a coarse-grained system. CG models are in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07. I tried to use check point file state.cpt to extend my simulation. The mdrun program can read to the check file. But it reported error like this: Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I check the *state.cpt* file using *gmxdump* and compare it with other checkpoint files that can be used for extending All-atom simulations. I found that in the CG check point file, some sections are missing: *box-v (3x3)* and *thermostat-integral*. I am not sure whether this missing sections cause my run crash. If it is, could any one tell me possible reasons that result in the loss of box-v and thermostat-integral and how to fix the problem? Your suggestions are greatly helpful and appreciated. Justin Zhang 在 2010年6月25日 下午4:45，张春雷 写道： > Information shown by gmxcheck: > > *Checking file state.cpt* > > # Atoms 9817 > Last frame -1 time 36.000 > > > Item#frames Timestep (ps) > Step 1 > Time 1 > Lambda 1 > Coords 1 > Velocities 1 > Forces 0 > Box 1 > > *Checking file state_prev.cpt* > > # Atoms 9817 > Last frame -1 time 359010.000 > > > Item#frames Timestep (ps) > Step 1 > Time 1 > Lambda 1 > Coords 1 > Velocities 1 > Forces 0 > Box 1 > > *Checking file md_360ns.trr* > trn version: GMX_trn_file (double precision) > Reading frame 0 time0.000 > # Atoms 9817 > Reading frame2000 time 30.000 > > > Item#frames Timestep (ps) > Step 2401150 > Time 2401150 > Lambda2401150 > Coords2401150 > Velocities2401150 > Forces 0 > Box 2401150 > > Is anything wrong? > > > 2010/6/25 Mark Abraham > > >> >> - Original Message - >> From: 张春雷 >> Date: Friday, June 25, 2010 16:46 >> Subject: Re: [gmx-users] P4_error for extending coarse grained MD >> simulations >> To: Discussion list for GROMACS users >> >> > The last .gro file only provides coordinates of the system. No velocity >> is recorded. Actually, what I attempt to achieve is a binary identical >> trajectory. So I think the velocity from the last step is critical. >> > >> > I have tried another approach in which the checkpoint file is >> neglected. >> > >> > $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g >> md_720ns.log >> > >> > It works. So the checkpoint file appears to contain some error. But it >> is generated by a normally finished production simulation. >> >> What does gmxcheck say about all the files involved? >> >> Mark >> >> >> > Have you encountered similar things? >> > >> > Thank you for your suggestions! >> > >> > >> > >> > 在 2010年6月25日 上午9:16，weixin 写道： >> >>> > >>> > How about using the last .gro file to continue your simulation? >>> > >>> > >>> > >>> > 2010/6/24 张春雷 >>> >>>> > Dear GMX-users, >>>> > >>>> > This is Justin. >>>> > I am performing coarse-grained simulation on a protein-lipid bilayer >>>> system. This is a MARTINI CG model. >>>> > I have successfully completed a 360ns simulation, during which the >>>> time step is 30 fs. >>>> > >>>> > I would like to extend the simulation to 1micro-second. The commands >>>> I used are: >>>> > >>>> > $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr >>>> > >>>> > $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr >>>> -g md_360ns.log -cpi state.cpt >>>> > >>>> > However, I received the following message: >>>> > >>>> > Checkpoint file is from part 1, new output files will be suffixed >>>> part0002. >>>> > Getting
[gmx-users] Re: P4_error for extending coarse grained MD simulations
Could anyone give me more suggestions? Many thanks! 2010/6/24 张春雷 > Dear GMX-users, > > This is Justin. > I am performing coarse-grained simulation on a protein-lipid bilayer > system. This is a MARTINI CG model. > I have successfully completed a 360ns simulation, during which the time > step is 30 fs. > > I would like to extend the simulation to 1micro-second. The commands I used > are: > > $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr > > $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g > md_360ns.log -cpi state.cpt > > However, I received the following message: > > Checkpoint file is from part 1, new output files will be suffixed part0002. > Getting Loaded... > Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) > > Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 > > Loaded with Money > > starting mdrun 'Protein in POPE bilayer' > 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). > step 1200, remaining runtime: 0 s > p0_6991: p4_error: interrupt SIGSEGV: 11 > > I have searched the mail-list, but found no similar report. I also search > through google, but no answer seems satisfactory. > > I once performed extending simulation for all atom simulation, and the > method mentioned above worked. > > Is anyone familiar with MARTINI CG simulation? > Could you give me some suggestions? > > Many thanks! > > Justin > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] P4_error for extending coarse grained MD simulations
Information shown by gmxcheck: *Checking file state.cpt* # Atoms 9817 Last frame -1 time 36.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 *Checking file state_prev.cpt* # Atoms 9817 Last frame -1 time 359010.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 *Checking file md_360ns.trr* trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 # Atoms 9817 Reading frame2000 time 30.000 Item#frames Timestep (ps) Step 2401150 Time 2401150 Lambda2401150 Coords2401150 Velocities2401150 Forces 0 Box 2401150 Is anything wrong? 2010/6/25 Mark Abraham > > > - Original Message - > From: 张春雷 > Date: Friday, June 25, 2010 16:46 > Subject: Re: [gmx-users] P4_error for extending coarse grained MD > simulations > To: Discussion list for GROMACS users > > > The last .gro file only provides coordinates of the system. No velocity > is recorded. Actually, what I attempt to achieve is a binary identical > trajectory. So I think the velocity from the last step is critical. > > > > I have tried another approach in which the checkpoint file is neglected. > > > > $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g > md_720ns.log > > > > It works. So the checkpoint file appears to contain some error. But it > is generated by a normally finished production simulation. > > What does gmxcheck say about all the files involved? > > Mark > > > > Have you encountered similar things? > > > > Thank you for your suggestions! > > > > > > > > 在 2010年6月25日 上午9:16，weixin 写道： > >> > >> > How about using the last .gro file to continue your simulation? >> > >> > >> > >> > 2010/6/24 张春雷 >> >>> > Dear GMX-users, >>> > >>> > This is Justin. >>> > I am performing coarse-grained simulation on a protein-lipid bilayer >>> system. This is a MARTINI CG model. >>> > I have successfully completed a 360ns simulation, during which the >>> time step is 30 fs. >>> > >>> > I would like to extend the simulation to 1micro-second. The commands I >>> used are: >>> > >>> > $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr >>> > >>> > $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr >>> -g md_360ns.log -cpi state.cpt >>> > >>> > However, I received the following message: >>> > >>> > Checkpoint file is from part 1, new output files will be suffixed >>> part0002. >>> > Getting Loaded... >>> > Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) >>> > >>> > Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 >>> > >>> > Loaded with Money >>> > >>> > starting mdrun 'Protein in POPE bilayer' >>> > 2400 steps, 72.0 ps (continuing from step 1200, 36.0 >>> ps). >>> > step 1200, remaining runtime: 0 s >>> > p0_6991: p4_error: interrupt SIGSEGV: 11 >>> > >>> > I have searched the mail-list, but found no similar report. I also >>> search through google, but no answer seems satisfactory. >>> > >>> > I once performed extending simulation for all atom simulation, and the >>> method mentioned above worked. >>> > >>> > Is anyone familiar with MARTINI CG simulation? >>> > Could you give me some suggestions? >>> > >>> > Many thanks! >>> > >>> > Justin >>> > >>> > -- >>> > gmx-users mailing listgmx-users@gromacs.org >>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<http://lists.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
Re: [gmx-users] Optimizing system size by moving from rectangular to hexagonal cells
I think you may try "trjconv -ur". 2010/6/25 Marc Baaden > > Dear All, > > Trying to optimize some simulation systems, I noticed that I could > actually gain quite some degrees of freedom by changing the xy > dimension of my simulation system from square/rectangular to hexagonal. > I wonder how one would do that in order to preserve at best the > properties of an already equilibrated system with a rectangular > xy-plane. Can Gromacs simply "cut" a hexagonal patch out of a periodic > simulation box with rectangular geometry? > Which tool would one use for this task? Editconf, with options eg > -c -box a b c -angles 120 120 90 ? > > Thank you very much in advance, > Marc Baaden > > -- > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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://lists.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] P4_error for extending coarse grained MD simulations
The last .gro file only provides coordinates of the system. No velocity is recorded. Actually, what I attempt to achieve is a binary identical trajectory. So I think the velocity from the last step is critical. I have tried another approach in which the checkpoint file is neglected. $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g md_720ns.log It works. So the checkpoint file appears to contain some error. But it is generated by a normally finished production simulation. Have you encountered similar things? Thank you for your suggestions! 在 2010年6月25日 上午9:16，weixin 写道： > > How about using the last .gro file to continue your simulation? > > > > 2010/6/24 张春雷 > >> Dear GMX-users, >> >> This is Justin. >> I am performing coarse-grained simulation on a protein-lipid bilayer >> system. This is a MARTINI CG model. >> I have successfully completed a 360ns simulation, during which the time >> step is 30 fs. >> >> I would like to extend the simulation to 1micro-second. The commands I >> used are: >> >> $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr >> >> $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g >> md_360ns.log -cpi state.cpt >> >> However, I received the following message: >> >> Checkpoint file is from part 1, new output files will be suffixed >> part0002. >> Getting Loaded... >> Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) >> >> Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 >> >> Loaded with Money >> >> starting mdrun 'Protein in POPE bilayer' >> 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). >> step 1200, remaining runtime: 0 s >> p0_6991: p4_error: interrupt SIGSEGV: 11 >> >> I have searched the mail-list, but found no similar report. I also search >> through google, but no answer seems satisfactory. >> >> I once performed extending simulation for all atom simulation, and the >> method mentioned above worked. >> >> Is anyone familiar with MARTINI CG simulation? >> Could you give me some suggestions? >> >> Many thanks! >> >> Justin >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.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://lists.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://lists.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] P4_error for extending coarse grained MD simulations
Dear GMX-users, This is Justin. I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model. I have successfully completed a 360ns simulation, during which the time step is 30 fs. I would like to extend the simulation to 1micro-second. The commands I used are: $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g md_360ns.log -cpi state.cpt However, I received the following message: Checkpoint file is from part 1, new output files will be suffixed part0002. Getting Loaded... Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I have searched the mail-list, but found no similar report. I also search through google, but no answer seems satisfactory. I once performed extending simulation for all atom simulation, and the method mentioned above worked. Is anyone familiar with MARTINI CG simulation? Could you give me some suggestions? Many thanks! Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
