Re: [gmx-users] wierd behavior of mdrun
Paymon Pirzadeh wrote: One more point: when I run the job interactively, although it works but date and time are wrong! step 0 step 100, will finish Wed Sep 16 16:16:00 2009 step 200, will finish Wed Sep 16 14:32:34 2009 step 300, will finish Wed Sep 16 13:57:51 2009 step 400, will finish Wed Sep 16 11:35:46 2009 step 500, will finish Wed Sep 16 11:50:12 2009 step 600, will finish Wed Sep 16 10:36:38 2009 step 700, will finish Wed Sep 16 09:44:04 2009 step 800, will finish Wed Sep 16 10:07:02 2009 step 900, will finish Wed Sep 16 09:29:25 2009 step 1000, will finish Wed Sep 16 08:59:19 2009 step 1100, will finish Wed Sep 16 09:20:06 2009 step 1200, will finish Wed Sep 16 08:55:47 2009 step 1300, will finish Wed Sep 16 09:13:38 2009 step 1400, will finish Wed Sep 16 08:53:15 2009 Is it a cluster related or GROMACS related issue? Is it important at all? That's just an estimate based on the elapsed wall time. If the source of elapsed wall time is unreliable or wrong, or the sample of wall time is too short, then the estimate will be wrong or vary widely accordingly. This prediction should stabilize over the course of the run. Mark ___ 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] wierd behavior of mdrun
How is it that the date and time is wrong? It is simply telling you that the simulation will be completed on Sep 16, using the time on the computer that the program is running on. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] wierd behavior of mdrun
One more point: when I run the job interactively, although it works but date and time are wrong! step 0 step 100, will finish Wed Sep 16 16:16:00 2009 step 200, will finish Wed Sep 16 14:32:34 2009 step 300, will finish Wed Sep 16 13:57:51 2009 step 400, will finish Wed Sep 16 11:35:46 2009 step 500, will finish Wed Sep 16 11:50:12 2009 step 600, will finish Wed Sep 16 10:36:38 2009 step 700, will finish Wed Sep 16 09:44:04 2009 step 800, will finish Wed Sep 16 10:07:02 2009 step 900, will finish Wed Sep 16 09:29:25 2009 step 1000, will finish Wed Sep 16 08:59:19 2009 step 1100, will finish Wed Sep 16 09:20:06 2009 step 1200, will finish Wed Sep 16 08:55:47 2009 step 1300, will finish Wed Sep 16 09:13:38 2009 step 1400, will finish Wed Sep 16 08:53:15 2009 Is it a cluster related or GROMACS related issue? Is it important at all? Payman On Wed, 2009-08-26 at 22:06 -0600, Paymon Pirzadeh wrote: I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluster shows that the job is running, also the processors are 100% engaged while I have no outputs! Here is my mdp file: title= Yo cpp = cpp include = -I../top define = -DPOSRES ; Run control integrator = md dt = 0.001 ;1 fs nsteps = 300 ;3 ns comm_mode= linear nstcomm = 1 ;Output control nstxout = 5000 nstlog = 5000 nstenergy= 5000 nstxtcout= 1500 nstvout = 5000 nstfout = 5000 xtc_grps = energygrps = ; Neighbour Searching nstlist = 10 ns_type = grid rlist= 0.9 pbc = xyz ; Electrostatistics coulombtype = PME rcoulomb = 0.9 ;epsilon_r= 1 ; Vdw vdwtype = cut-off rvdw = 1.2 DispCorr = EnerPres ;Ewald fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 optimize_fft= yes ; Temperature coupling tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t= 0.1 ref_t= 275 ; Pressure Coupling Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 5.5e-5 ;ref_p= 1.0 gen_vel = yes gen_temp = 275 gen_seed = 173529 constraint-algorithm = Lincs constraints = all-bonds lincs-order = 4 I am not sure where things go wrong! Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ 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] wierd behavior of mdrun
I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluster shows that the job is running, also the processors are 100% engaged while I have no outputs! Here is my mdp file: title= Yo cpp = cpp include = -I../top define = -DPOSRES ; Run control integrator = md dt = 0.001 ;1 fs nsteps = 300 ;3 ns comm_mode= linear nstcomm = 1 ;Output control nstxout = 5000 nstlog = 5000 nstenergy= 5000 nstxtcout= 1500 nstvout = 5000 nstfout = 5000 xtc_grps = energygrps = ; Neighbour Searching nstlist = 10 ns_type = grid rlist= 0.9 pbc = xyz ; Electrostatistics coulombtype = PME rcoulomb = 0.9 ;epsilon_r= 1 ; Vdw vdwtype = cut-off rvdw = 1.2 DispCorr = EnerPres ;Ewald fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 optimize_fft= yes ; Temperature coupling tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t= 0.1 ref_t= 275 ; Pressure Coupling Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 5.5e-5 ;ref_p= 1.0 gen_vel = yes gen_temp = 275 gen_seed = 173529 constraint-algorithm = Lincs constraints = all-bonds lincs-order = 4 I am not sure where things go wrong! Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ 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] wierd behavior of mdrun
Paymon Pirzadeh wrote: I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluster shows that the job is running, also the processors are 100% engaged while I have no outputs! Check that a short version of this job runs fine on a local machine. Probably you are having some problem with a file system and/or its buffering. Inspect your quotas. Talk to your system admins. Mark Here is my mdp file: title= Yo cpp = cpp include = -I../top define = -DPOSRES ; Run control integrator = md dt = 0.001 ;1 fs nsteps = 300 ;3 ns comm_mode= linear nstcomm = 1 ;Output control nstxout = 5000 nstlog = 5000 nstenergy= 5000 nstxtcout= 1500 nstvout = 5000 nstfout = 5000 xtc_grps = energygrps = ; Neighbour Searching nstlist = 10 ns_type = grid rlist= 0.9 pbc = xyz ; Electrostatistics coulombtype = PME rcoulomb = 0.9 ;epsilon_r= 1 ; Vdw vdwtype = cut-off rvdw = 1.2 DispCorr = EnerPres ;Ewald fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 optimize_fft= yes ; Temperature coupling tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t= 0.1 ref_t= 275 ; Pressure Coupling Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 5.5e-5 ;ref_p= 1.0 gen_vel = yes gen_temp = 275 gen_seed = 173529 constraint-algorithm = Lincs constraints = all-bonds lincs-order = 4 I am not sure where things go wrong! Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ 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
