Re: [gmx-users] Regarding manual velocity generation in simulation
On Feb 5, 2013, at 8:22 AM, bipin singh wrote: Hello All, Please let me know whether is it possible to manually assign the velocity for each atom in the simulation instead of generating through gen_vel option. If the preceision of a gro-file is sufficient you can use such for manually setting velocities of individual atoms. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] MPI oversubscription
Hi, I am using the latest git version of gromacs, compiled with gcc 4.6.2 and openmpi 1.6.3. I start the program using the usual mpirun -np 8 mdrun_mpi ... This always leads to a warning: Using 1 MPI process WARNING: On node 0: oversubscribing the available 0 logical CPU cores per node with 1 MPI processes. Checking the processes confirms that there is only one of the 8 available cores used. Running mdrun_mpi with an additional debug -1: Detected 0 processors, will use this as the number of supported hardware threads. hw_opt: nt 0 ntmpi 0 ntomp 1 ntomp_pme 1 gpu_id '' 0 CPUs detected, but 8 was returned by CPU_COUNTIn gmx_setup_nodecomm: hostname 'myComputerName', hostnum 0 ... 0 CPUs detected, but 8 was returned by CPU_COUNTOn rank 0, thread 0, core 0 the affinity setting returned 0 I also made another try by compiling gromacs using some experimental version of gcc 4.8, which did not help in this case. Is this a known problem? Obviously gromacs detects the right value with CPU_COUNT, why is it not just taking that value? Best regards, Christian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Expanded Ensemble and Gromacs 4.6
Hi, I am trying to use the Expanded Ensemble (EE) method to compute the free energy of solvation of a small organic molecule. Basically I am playing around but I cannot get the simulations to run. Here are my EE and free energy settings: %--- free-energy = expanded ; Expanded ensemble couple-moltype = C1X ; Molecule to introduce couple-lambda0 = none ; Go from no interactions with solvent... couple-lambda1 = vdw-q ; ...to full interactions couple-intramol = no; Do not decouple internal interactions init_lambda_state = 0 ; Start from the first column of the lambda vectors delta-lambda= 0 ; No increments in lambda nstdhdl = 100 ; Frequency for writing dH/dlambda coul-lambdas= 0.0 0.25 0.5 0.75 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.7 0.8 0.9 1.0 dhdl-print-energy = yes ; Include total energy in the dhdl file sc-alpha= 0.5 ; Soft core alpha parameter sc-power= 1 ; Power of lambda in soft core function sc-r-power = 6 ; Power of radial term in the soft core function sc-sigma= 0.3 ; Soft core sigma sc-coul = no; No soft core for Coulomb separate-dhdl-file = yes ; Seperate dhdl files dhdl-derivatives= yes ; Print derivatives of the Hamiltonian ; expanded ensemble variables nstexpanded = 100 ; Number of steps between attempts to change the Hamiltonian lmc-stats = wang-landau ; WL algorithm to explore state space lmc-move= gibbs ; Decides which state to move to lmc-weights-equil = number-steps ; EE weight updating stops after... weight-equil-number-steps = 500 ; ...10ns of simulation ; Seed for Monte Carlo in lambda space lmc-seed= 1993 lmc-repeats = 1 lmc-gibbsdelta = -1 lmc-forced-nstart = 0 symmetrized-transition-matrix = no nst-transition-matrix = -1 mininum-var-min = 100 wl-scale= 0.6 wl-ratio= 0.8 init-wl-delta = 1 wl-oneovert = yes %--- Besides this I use LINCS to constrain all bonds, sd-integrator and a normal cut-off scheme with a 1 fs time step. However, once I try to run the files on the cluster I always end up with LINCS warnings and after a few seconds the program crashes due to too many LINCS warnings. If I increase the time step to 2 fs I run into problems SETTLE for the water. I always start from a nice structure that is taken as the final snap shot from a simple 1 ns MD simulation of my system. What could be the problem? If I use free_energy = yes instead of EE things work fine. Did I perhaps mess up the EE settings or something? Thanks in advance. Best, Joakim -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Join my network on LinkedIn
LinkedIn Yi Gao requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Yi Accept invitation from Yi Gao http://www.linkedin.com/e/-85v1n9-hcsylpal-5g/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I437135640_16/0UcDpKqiRzolZKqiRybmRSrCBvrmRLoORIrmkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYSclYMd3oRcP4TcPh9bSVxhmNpm4NKbPoUdP8OdPgPcPALrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=falsetok=24EnCx7xnaUlA1 View profile of Yi Gao http://www.linkedin.com/e/-85v1n9-hcsylpal-5g/rso/67557412/BcCF/name/15686615_I437135640_16/?hs=falsetok=2FfVbJj9LaUlA1 -- You are receiving Invitation emails. This email was intended for Chinmay Das. Learn why this is included: http://www.linkedin.com/e/-85v1n9-hcsylpal-5g/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=falsetok=0Iay4QBYbaUlA1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] MPI oversubscription
Hi, This looks like our CPU detection code failed and the result is not handled properly. What hardware are you running on? Could you mail the 10 lines from the md.log file following: Detecting CPU-specific acceleration.? Cheers, Berk Date: Tue, 5 Feb 2013 11:38:53 +0100 From: hypo...@googlemail.com To: gmx-users@gromacs.org Subject: [gmx-users] MPI oversubscription Hi, I am using the latest git version of gromacs, compiled with gcc 4.6.2 and openmpi 1.6.3. I start the program using the usual mpirun -np 8 mdrun_mpi ... This always leads to a warning: Using 1 MPI process WARNING: On node 0: oversubscribing the available 0 logical CPU cores per node with 1 MPI processes. Checking the processes confirms that there is only one of the 8 available cores used. Running mdrun_mpi with an additional debug -1: Detected 0 processors, will use this as the number of supported hardware threads. hw_opt: nt 0 ntmpi 0 ntomp 1 ntomp_pme 1 gpu_id '' 0 CPUs detected, but 8 was returned by CPU_COUNTIn gmx_setup_nodecomm: hostname 'myComputerName', hostnum 0 ... 0 CPUs detected, but 8 was returned by CPU_COUNTOn rank 0, thread 0, core 0 the affinity setting returned 0 I also made another try by compiling gromacs using some experimental version of gcc 4.8, which did not help in this case. Is this a known problem? Obviously gromacs detects the right value with CPU_COUNT, why is it not just taking that value? Best regards, Christian -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] MPI oversubscription
From the .log file: Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz Family: 6 Model: 42 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE From /proc/cpuinfo (8 entries like this in total): processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 42 model name : Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz stepping: 7 microcode : 0x28 cpu MHz : 1600.000 cache size : 8192 KB physical id : 0 siblings: 8 core id : 0 cpu cores : 4 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmper f pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 popcnt tsc_deadline_timer aes xsave avx lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid bogomips: 6784.04 clflush size: 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: It also does not work on the local cluster, the output in the .log file is: Detecting CPU-specific acceleration. Present hardware specification: Vendor: AuthenticAMD Brand: AMD Opteron(TM) Processor 6220 Family: 21 Model: 1 Stepping: 2 Features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop Acceleration most likely to fit this hardware: AVX_128_FMA Acceleration selected at GROMACS compile time: AVX_128_FMA Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE I am not too sure about the details for that setup, but the brand looks about right. Do you need any other information? Thanks for looking into it! 2013/2/5 Berk Hess g...@hotmail.com Hi, This looks like our CPU detection code failed and the result is not handled properly. What hardware are you running on? Could you mail the 10 lines from the md.log file following: Detecting CPU-specific acceleration.? Cheers, Berk Date: Tue, 5 Feb 2013 11:38:53 +0100 From: hypo...@googlemail.com To: gmx-users@gromacs.org Subject: [gmx-users] MPI oversubscription Hi, I am using the latest git version of gromacs, compiled with gcc 4.6.2 and openmpi 1.6.3. I start the program using the usual mpirun -np 8 mdrun_mpi ... This always leads to a warning: Using 1 MPI process WARNING: On node 0: oversubscribing the available 0 logical CPU cores per node with 1 MPI processes. Checking the processes confirms that there is only one of the 8 available cores used. Running mdrun_mpi with an additional debug -1: Detected 0 processors, will use this as the number of supported hardware threads. hw_opt: nt 0 ntmpi 0 ntomp 1 ntomp_pme 1 gpu_id '' 0 CPUs detected, but 8 was returned by CPU_COUNTIn gmx_setup_nodecomm: hostname 'myComputerName', hostnum 0 ... 0 CPUs detected, but 8 was returned by CPU_COUNTOn rank 0, thread 0, core 0 the affinity setting returned 0 I also made another try by compiling gromacs using some experimental version of gcc 4.8, which did not help in this case. Is this a known problem? Obviously gromacs detects the right value with CPU_COUNT, why is it not just taking that value? Best regards, Christian -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
RE: [gmx-users] MPI oversubscription
Hi, This is the same cpu I have in my workstation and this case should not cause any problems. Which operating system and version are you using? If you know a bit about programming, could you check what goes wrong in get_nthreads_hw_avail in src/gmxlib/gmx_detect_hardware.c ? Add after the four ret = at line 434, 436, 438 and 440: printf(case 1 ret = %d\n,ret); and replace 1 by different numbers. Thus you can check if one of the 4 cases returns 0 or none of the cases is called. Cheers, Berk Date: Tue, 5 Feb 2013 13:45:02 +0100 Subject: Re: [gmx-users] MPI oversubscription From: hypo...@googlemail.com To: gmx-users@gromacs.org From the .log file: Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz Family: 6 Model: 42 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE From /proc/cpuinfo (8 entries like this in total): processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 42 model name : Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz stepping : 7 microcode : 0x28 cpu MHz : 1600.000 cache size : 8192 KB physical id : 0 siblings : 8 core id : 0 cpu cores : 4 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmper f pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 popcnt tsc_deadline_timer aes xsave avx lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid bogomips : 6784.04 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: It also does not work on the local cluster, the output in the .log file is: Detecting CPU-specific acceleration. Present hardware specification: Vendor: AuthenticAMD Brand: AMD Opteron(TM) Processor 6220 Family: 21 Model: 1 Stepping: 2 Features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop Acceleration most likely to fit this hardware: AVX_128_FMA Acceleration selected at GROMACS compile time: AVX_128_FMA Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE I am not too sure about the details for that setup, but the brand looks about right. Do you need any other information? Thanks for looking into it! 2013/2/5 Berk Hess g...@hotmail.com Hi, This looks like our CPU detection code failed and the result is not handled properly. What hardware are you running on? Could you mail the 10 lines from the md.log file following: Detecting CPU-specific acceleration.? Cheers, Berk Date: Tue, 5 Feb 2013 11:38:53 +0100 From: hypo...@googlemail.com To: gmx-users@gromacs.org Subject: [gmx-users] MPI oversubscription Hi, I am using the latest git version of gromacs, compiled with gcc 4.6.2 and openmpi 1.6.3. I start the program using the usual mpirun -np 8 mdrun_mpi ... This always leads to a warning: Using 1 MPI process WARNING: On node 0: oversubscribing the available 0 logical CPU cores per node with 1 MPI processes. Checking the processes confirms that there is only one of the 8 available cores used. Running mdrun_mpi with an additional debug -1: Detected 0 processors, will use this as the number of supported hardware threads. hw_opt: nt 0 ntmpi 0 ntomp 1 ntomp_pme 1 gpu_id '' 0 CPUs detected, but 8 was returned by CPU_COUNTIn gmx_setup_nodecomm: hostname 'myComputerName', hostnum 0 ... 0 CPUs detected, but 8 was returned by CPU_COUNTOn rank 0, thread 0, core 0 the affinity setting returned 0 I also made another try by compiling gromacs using some experimental version of gcc 4.8, which did not help in this case. Is this a known problem? Obviously gromacs detects the right value with CPU_COUNT, why is it not just taking that value? Best regards, Christian -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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
Re: [gmx-users] MPI oversubscription
None of the variables referenced here are set on my system, the print statements are never executed. What I did: printf(Checking which processor variable is set); #if defined(_SC_NPROCESSORS_ONLN) ret = sysconf(_SC_NPROCESSORS_ONLN); printf(case 1 ret = %d\n,ret); #elif defined(_SC_NPROC_ONLN) ret = sysconf(_SC_NPROC_ONLN); printf(case 2 ret = %d\n,ret); #elif defined(_SC_NPROCESSORS_CONF) ret = sysconf(_SC_NPROCESSORS_CONF); printf(case 3 ret = %d\n,ret); #elif defined(_SC_NPROC_CONF) ret = sysconf(_SC_NPROC_CONF); printf(case 4 ret = %d\n,ret); #endif /* End of check for sysconf argument values */ From /etc/issue: Welcome to openSUSE 12.2 Mantis - Kernel \r (\l) From uname -a: Linux kafka 3.4.11-2.16-desktop #1 SMP PREEMPT Wed Sep 26 17:05:00 UTC 2012 (259fc87) x86_64 x86_64 x86_64 GNU/Linux 2013/2/5 Berk Hess g...@hotmail.com Hi, This is the same cpu I have in my workstation and this case should not cause any problems. Which operating system and version are you using? If you know a bit about programming, could you check what goes wrong in get_nthreads_hw_avail in src/gmxlib/gmx_detect_hardware.c ? Add after the four ret = at line 434, 436, 438 and 440: printf(case 1 ret = %d\n,ret); and replace 1 by different numbers. Thus you can check if one of the 4 cases returns 0 or none of the cases is called. Cheers, Berk Date: Tue, 5 Feb 2013 13:45:02 +0100 Subject: Re: [gmx-users] MPI oversubscription From: hypo...@googlemail.com To: gmx-users@gromacs.org From the .log file: Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz Family: 6 Model: 42 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE From /proc/cpuinfo (8 entries like this in total): processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 42 model name : Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz stepping : 7 microcode : 0x28 cpu MHz : 1600.000 cache size : 8192 KB physical id : 0 siblings : 8 core id : 0 cpu cores : 4 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmper f pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 popcnt tsc_deadline_timer aes xsave avx lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid bogomips : 6784.04 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: It also does not work on the local cluster, the output in the .log file is: Detecting CPU-specific acceleration. Present hardware specification: Vendor: AuthenticAMD Brand: AMD Opteron(TM) Processor 6220 Family: 21 Model: 1 Stepping: 2 Features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop Acceleration most likely to fit this hardware: AVX_128_FMA Acceleration selected at GROMACS compile time: AVX_128_FMA Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE I am not too sure about the details for that setup, but the brand looks about right. Do you need any other information? Thanks for looking into it! 2013/2/5 Berk Hess g...@hotmail.com Hi, This looks like our CPU detection code failed and the result is not handled properly. What hardware are you running on? Could you mail the 10 lines from the md.log file following: Detecting CPU-specific acceleration.? Cheers, Berk Date: Tue, 5 Feb 2013 11:38:53 +0100 From: hypo...@googlemail.com To: gmx-users@gromacs.org Subject: [gmx-users] MPI oversubscription Hi, I am using the latest git version of gromacs, compiled with gcc 4.6.2 and openmpi 1.6.3. I start the program using the usual mpirun -np 8 mdrun_mpi ... This always leads to a warning: Using 1 MPI process WARNING: On node 0: oversubscribing the available 0 logical CPU cores per node with 1 MPI processes. Checking the processes confirms that there is only one of the 8 available cores used. Running mdrun_mpi with an additional debug -1: Detected 0 processors, will use this as the number
RE: [gmx-users] MPI oversubscription
OK, then this is an unhandled case.
Strange, because I am also running OpenSUSE 12.2 with the same CPU, but use gcc
4.7.1.
I will file a bug report on redmine.
Could you also post the header of md.log which gives all configuration
information?
To make it work for now, you can insert immediately after #ifdef GMX_OMPENMP:
if (ret = 0)
{
ret = gmx_omp_get_num_procs();
}
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:27:44 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
None of the variables referenced here are set on my system, the print
statements are never executed.
What I did:
printf(Checking which processor variable is set);
#if defined(_SC_NPROCESSORS_ONLN)
ret = sysconf(_SC_NPROCESSORS_ONLN);
printf(case 1 ret = %d\n,ret);
#elif defined(_SC_NPROC_ONLN)
ret = sysconf(_SC_NPROC_ONLN);
printf(case 2 ret = %d\n,ret);
#elif defined(_SC_NPROCESSORS_CONF)
ret = sysconf(_SC_NPROCESSORS_CONF);
printf(case 3 ret = %d\n,ret);
#elif defined(_SC_NPROC_CONF)
ret = sysconf(_SC_NPROC_CONF);
printf(case 4 ret = %d\n,ret);
#endif /* End of check for sysconf argument values */
From /etc/issue:
Welcome to openSUSE 12.2 Mantis - Kernel \r (\l)
From uname -a:
Linux kafka 3.4.11-2.16-desktop #1 SMP PREEMPT Wed Sep 26 17:05:00 UTC 2012
(259fc87) x86_64 x86_64 x86_64 GNU/Linux
2013/2/5 Berk Hess g...@hotmail.com
Hi,
This is the same cpu I have in my workstation and this case should not
cause any problems.
Which operating system and version are you using?
If you know a bit about programming, could you check what goes wrong in
get_nthreads_hw_avail
in src/gmxlib/gmx_detect_hardware.c ?
Add after the four ret = at line 434, 436, 438 and 440:
printf(case 1 ret = %d\n,ret);
and replace 1 by different numbers.
Thus you can check if one of the 4 cases returns 0 or none of the cases
is called.
Cheers,
Berk
Date: Tue, 5 Feb 2013 13:45:02 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
From the .log file:
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Family: 6 Model: 42 Stepping: 7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc
pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
From /proc/cpuinfo (8 entries like this in total):
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 42
model name : Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
stepping : 7
microcode : 0x28
cpu MHz : 1600.000
cache size : 8192 KB
physical id : 0
siblings : 8
core id : 0
cpu cores : 4
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology
nonstop_tsc aperfmper
f pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm
pcid
sse4_1 sse4_2 popcnt tsc_deadline_timer aes xsave avx lahf_lm ida arat
epb
xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid
bogomips : 6784.04
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
It also does not work on the local cluster, the output in the .log file
is:
Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: AuthenticAMD
Brand: AMD Opteron(TM) Processor 6220
Family: 21 Model: 1 Stepping: 2
Features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm misalignsse
mmx
msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1
sse4.2 ssse3 xop
Acceleration most likely to fit this hardware: AVX_128_FMA
Acceleration selected at GROMACS compile time: AVX_128_FMA
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
I am not too sure about the details for that setup, but the brand looks
about right.
Do you need any other information?
Thanks for looking into it!
2013/2/5 Berk Hess g...@hotmail.com
Hi,
This looks like our CPU detection code failed and the result is not
handled properly.
What hardware are you running on?
Could you mail the 10 lines from the md.log file following: Detecting
CPU-specific acceleration.?
Cheers,
Berk
Re: [gmx-users] Membrane simulation - error during EM after inflation step
On 2/4/13 11:09 PM, John K wrote: Hello Justin, Thank you for providing a tutorial for membrane simulation. I am doing membrane simulation by following your tutorial. When I tried to do energy minimization after inflating the system i got the following result. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.6157550e+17 Maximum force =inf on atom 2093 Norm of force =inf So the system is not converged well. I checked the output .gro file the protein came completely out of the bilayer. I tried to fix the problem by increasing the -fc value to 100 but still problem continues. Will you please tell me what will be the reason behind this problem and how to fix it. If the protein is completely out of the bilayer, that means you haven't built the system properly. EM will not cause massive displacement of any species, so a protein floating out in the middle of nowhere indicates it is incorrectly centered within the unit cell. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] acpype
On 2/5/13 2:10 AM, az kalsom wrote: hi, i wanted to say i am not able to make acpype for me, i am following the tutorial , http://code.google.com/p/acpype/wiki/HowToUse but i am still geeting the error that this comand is not found anybody please help me It's just a Python script, so you can execute it from anywhere. The how-to indicates how you can use a softlink to some root-level directory if you want, otherwise just run the script locally. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Error in BlueGene
On Mon, Feb 4, 2013 at 5:18 PM, Cintia C. Vequi-Suplicy cin...@if.usp.brwrote: Hello David, I think it is the pressure. I would think the mentions of pressure are just one of the symptoms. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up. You seem to have somewhat more than 100K atoms, which is a bit over 200 atoms/processor for 512 processors. That's down the low end of GROMACS scaling limits. I asked you earlier to try running with the same number of processors on the BlueGene as you do locally, and to report the command lines you were using for the whole transfer and restart process. This will allow us to see if the problem is in how DD is treating your system, or how you are managing the transfer between hardware. Until then, nobody can tell anything. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] MPI oversubscription
Head of .log:
Gromacs version:VERSION 5.0-dev-20121213-e1fcb0a-dirty
GIT SHA1 hash: e1fcb0a3d2768a8bb28c2e4e8012123ce773e18c (dirty)
Precision: single
MPI library:MPI
OpenMP support: disabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library:fftw-3.3.2-sse2
Large file support: disabled
RDTSCP usage: enabled
Built on: Tue Feb 5 10:58:32 CET 2013
Built by: christian@k [CMAKE]
Build OS/arch: Linux 3.4.11-2.16-desktop x86_64
Build CPU vendor: GenuineIntel
Build CPU brand:Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Build CPU family: 6 Model: 42 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2
ssse3 tdt
C compiler: /home/christian/opt/bin/mpicc GNU gcc (GCC) 4.8.0
20120618 (experimental)
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
-DNDEBUG
C++ compiler: /home/christian/opt/bin/mpiCC GNU g++ (GCC) 4.8.0
20120618 (experimental)
C++ compiler flags: -mavx -std=c++0x -Wextra
-Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused
-Wunused-value -Wno-unknown-pragmas -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
I will try your workaround, thanks!
2013/2/5 Berk Hess g...@hotmail.com
OK, then this is an unhandled case.
Strange, because I am also running OpenSUSE 12.2 with the same CPU, but
use gcc 4.7.1.
I will file a bug report on redmine.
Could you also post the header of md.log which gives all configuration
information?
To make it work for now, you can insert immediately after #ifdef
GMX_OMPENMP:
if (ret = 0)
{
ret = gmx_omp_get_num_procs();
}
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:27:44 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
None of the variables referenced here are set on my system, the print
statements are never executed.
What I did:
printf(Checking which processor variable is set);
#if defined(_SC_NPROCESSORS_ONLN)
ret = sysconf(_SC_NPROCESSORS_ONLN);
printf(case 1 ret = %d\n,ret);
#elif defined(_SC_NPROC_ONLN)
ret = sysconf(_SC_NPROC_ONLN);
printf(case 2 ret = %d\n,ret);
#elif defined(_SC_NPROCESSORS_CONF)
ret = sysconf(_SC_NPROCESSORS_CONF);
printf(case 3 ret = %d\n,ret);
#elif defined(_SC_NPROC_CONF)
ret = sysconf(_SC_NPROC_CONF);
printf(case 4 ret = %d\n,ret);
#endif /* End of check for sysconf argument values */
From /etc/issue:
Welcome to openSUSE 12.2 Mantis - Kernel \r (\l)
From uname -a:
Linux kafka 3.4.11-2.16-desktop #1 SMP PREEMPT Wed Sep 26 17:05:00 UTC
2012
(259fc87) x86_64 x86_64 x86_64 GNU/Linux
2013/2/5 Berk Hess g...@hotmail.com
Hi,
This is the same cpu I have in my workstation and this case should not
cause any problems.
Which operating system and version are you using?
If you know a bit about programming, could you check what goes wrong in
get_nthreads_hw_avail
in src/gmxlib/gmx_detect_hardware.c ?
Add after the four ret = at line 434, 436, 438 and 440:
printf(case 1 ret = %d\n,ret);
and replace 1 by different numbers.
Thus you can check if one of the 4 cases returns 0 or none of the cases
is called.
Cheers,
Berk
Date: Tue, 5 Feb 2013 13:45:02 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
From the .log file:
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Family: 6 Model: 42 Stepping: 7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc
pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
tdt
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
From /proc/cpuinfo (8 entries like this in total):
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 42
model name : Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
stepping : 7
microcode : 0x28
cpu MHz : 1600.000
cache size : 8192 KB
physical id : 0
siblings : 8
core id : 0
cpu cores : 4
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht
RE: [gmx-users] MPI oversubscription
One last thing:
Maybe a macro is not set, but we can actually query the number of processors.
Could you replace the conditional that gets triggered on my machine:
#if defined(_SC_NPROCESSORS_ONLN)
to
#if 1
So we can check if the actual sysconf call works or not?
My workaround won't work without OpenMP.
Did you disable that manually?
Also large file support is not turned on.
It seems like your build setup is somehow messed up and lot of features are not
found.
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:52:17 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
Head of .log:
Gromacs version: VERSION 5.0-dev-20121213-e1fcb0a-dirty
GIT SHA1 hash: e1fcb0a3d2768a8bb28c2e4e8012123ce773e18c (dirty)
Precision: single
MPI library: MPI
OpenMP support: disabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library: fftw-3.3.2-sse2
Large file support: disabled
RDTSCP usage: enabled
Built on: Tue Feb 5 10:58:32 CET 2013
Built by: christian@k [CMAKE]
Build OS/arch: Linux 3.4.11-2.16-desktop x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Build CPU family: 6 Model: 42 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2
ssse3 tdt
C compiler: /home/christian/opt/bin/mpicc GNU gcc (GCC) 4.8.0
20120618 (experimental)
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
-DNDEBUG
C++ compiler: /home/christian/opt/bin/mpiCC GNU g++ (GCC) 4.8.0
20120618 (experimental)
C++ compiler flags: -mavx -std=c++0x -Wextra
-Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused
-Wunused-value -Wno-unknown-pragmas -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
I will try your workaround, thanks!
2013/2/5 Berk Hess g...@hotmail.com
OK, then this is an unhandled case.
Strange, because I am also running OpenSUSE 12.2 with the same CPU, but
use gcc 4.7.1.
I will file a bug report on redmine.
Could you also post the header of md.log which gives all configuration
information?
To make it work for now, you can insert immediately after #ifdef
GMX_OMPENMP:
if (ret = 0)
{
ret = gmx_omp_get_num_procs();
}
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:27:44 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
None of the variables referenced here are set on my system, the print
statements are never executed.
What I did:
printf(Checking which processor variable is set);
#if defined(_SC_NPROCESSORS_ONLN)
ret = sysconf(_SC_NPROCESSORS_ONLN);
printf(case 1 ret = %d\n,ret);
#elif defined(_SC_NPROC_ONLN)
ret = sysconf(_SC_NPROC_ONLN);
printf(case 2 ret = %d\n,ret);
#elif defined(_SC_NPROCESSORS_CONF)
ret = sysconf(_SC_NPROCESSORS_CONF);
printf(case 3 ret = %d\n,ret);
#elif defined(_SC_NPROC_CONF)
ret = sysconf(_SC_NPROC_CONF);
printf(case 4 ret = %d\n,ret);
#endif /* End of check for sysconf argument values */
From /etc/issue:
Welcome to openSUSE 12.2 Mantis - Kernel \r (\l)
From uname -a:
Linux kafka 3.4.11-2.16-desktop #1 SMP PREEMPT Wed Sep 26 17:05:00 UTC
2012
(259fc87) x86_64 x86_64 x86_64 GNU/Linux
2013/2/5 Berk Hess g...@hotmail.com
Hi,
This is the same cpu I have in my workstation and this case should not
cause any problems.
Which operating system and version are you using?
If you know a bit about programming, could you check what goes wrong in
get_nthreads_hw_avail
in src/gmxlib/gmx_detect_hardware.c ?
Add after the four ret = at line 434, 436, 438 and 440:
printf(case 1 ret = %d\n,ret);
and replace 1 by different numbers.
Thus you can check if one of the 4 cases returns 0 or none of the cases
is called.
Cheers,
Berk
Date: Tue, 5 Feb 2013 13:45:02 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
From the .log file:
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Family: 6 Model: 42 Stepping: 7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc
pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
tdt
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256
Table routines
[gmx-users] error in running command
Dear Sir/ Madam I am using gromacs for simulation and has the following while running the command for grompp Expected integer argument for option -maxwarn . I do not want use maxwarn to bypass the error. I request you to kindly help me out to debug the error. Regards Arunima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Expanded Ensemble and Gromacs 4.6
Hi, Joakim- Expanded ensemble is still a bit experimental. I don't immediately see any problem that jump right out, but if you go to http://redmine.gromacs.org/ and file a bug report, including giving example files that cause the problem, I can take a look at it. On Tue, Feb 5, 2013 at 6:00 AM, Joakim Jämbeck jamb...@me.com wrote: Hi, I am trying to use the Expanded Ensemble (EE) method to compute the free energy of solvation of a small organic molecule. Basically I am playing around but I cannot get the simulations to run. Here are my EE and free energy settings: %--- free-energy = expanded ; Expanded ensemble couple-moltype = C1X ; Molecule to introduce couple-lambda0 = none ; Go from no interactions with solvent... couple-lambda1 = vdw-q ; ...to full interactions couple-intramol = no; Do not decouple internal interactions init_lambda_state = 0 ; Start from the first column of the lambda vectors delta-lambda= 0 ; No increments in lambda nstdhdl = 100 ; Frequency for writing dH/dlambda coul-lambdas= 0.0 0.25 0.5 0.75 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.7 0.8 0.9 1.0 dhdl-print-energy = yes ; Include total energy in the dhdl file sc-alpha= 0.5 ; Soft core alpha parameter sc-power= 1 ; Power of lambda in soft core function sc-r-power = 6 ; Power of radial term in the soft core function sc-sigma= 0.3 ; Soft core sigma sc-coul = no; No soft core for Coulomb separate-dhdl-file = yes ; Seperate dhdl files dhdl-derivatives= yes ; Print derivatives of the Hamiltonian ; expanded ensemble variables nstexpanded = 100 ; Number of steps between attempts to change the Hamiltonian lmc-stats = wang-landau ; WL algorithm to explore state space lmc-move= gibbs ; Decides which state to move to lmc-weights-equil = number-steps ; EE weight updating stops after... weight-equil-number-steps = 500 ; ...10ns of simulation ; Seed for Monte Carlo in lambda space lmc-seed= 1993 lmc-repeats = 1 lmc-gibbsdelta = -1 lmc-forced-nstart = 0 symmetrized-transition-matrix = no nst-transition-matrix = -1 mininum-var-min = 100 wl-scale= 0.6 wl-ratio= 0.8 init-wl-delta = 1 wl-oneovert = yes %--- Besides this I use LINCS to constrain all bonds, sd-integrator and a normal cut-off scheme with a 1 fs time step. However, once I try to run the files on the cluster I always end up with LINCS warnings and after a few seconds the program crashes due to too many LINCS warnings. If I increase the time step to 2 fs I run into problems SETTLE for the water. I always start from a nice structure that is taken as the final snap shot from a simple 1 ns MD simulation of my system. What could be the problem? If I use free_energy = yes instead of EE things work fine. Did I perhaps mess up the EE settings or something? Thanks in advance. Best, Joakim -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Error in BlueGene
Mark, Thank you for your answer. I have already tried to run with several numbers of processors from 8 to 512 and I always got the same error. And I transfer the simulation to the BlueGene in two different ways. In both ways, I got the same error. They were the following: 1) only using the .gro file after the simulation on my local cluster with the velocities, generate a new .tpr using the md.mdp I sent before. And the use this .tpr file to run in the bluegene. The commands were these: grompp -f md.mdp -c min_dppc.gro -p dppc512.top -o dppc10ns.tpr /*(this was done in my computer) and then in the bgp, I submitted the following script: #@ job_name = dppc_001ps #@ comment = bilayer continuacao gauss com cpi #@ error = $(job_name).$(jobid).out #@ output = $(job_name).$(jobid).out #@ environment = COPY_ALL #@ wall_clock_limit = 80:00:00 #@ notification = error #@ job_type = bluegene #@ class = compute #@ bg_size = 128 #@ queue /bgsys/drivers/ppcfloor/bin/mpirun -np 512 -exe /opt/apps/gromacs/4.5.5/bin/mdrun -args -s dppc10.tpr -v -mode VN 2) I used the .tpr and the state.cpt from the simulation on my local cluster to restart the simulation on the bluegene with more nodes. And the script I used was: #@ job_name = gromacs_dppc #@ comment = bilayer #@ error = $(job_name).$(jobid).out #@ output = $(job_name).$(jobid).out #@ environment = COPY_ALL #@ wall_clock_limit = 80:00:00 #@ notification = error #@ job_type = bluegene #@ class = compute #@ bg_size = 128 #@ queue /bgsys/drivers/ppcfloor/bin/mpirun -np 512 -exe /opt/apps/gromacs/4.5.5/bin/mdrun -args -cpi state.cpt -s dppc_min.tpr -v -mode VN In both ways, I got the same error. Cheers, Cíntia md.mdp integrator = md tinit= 0.0 dt = 0.002 nsteps = 500 nstcomm = 5 comm-grps= Other SOL nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy= 1000 nstxtcout= 1000 xtc_precision= 1000 xtc-grps = energygrps = Other SOL nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = reaction-field rcoulomb = 1.4 epsilon_rf = 66 vdw_type = cut-off rvdw = 1.4 DispCorr = No tcoupl = v-rescale tc-grps = Other SOL tau_t= 0.4 0.4 ref_t= 296 296 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 0.2 0.2 compressibility = 4.51e-5 4.51e-5 ref_p= 1.0 1.0 constraints = hbonds constraint_algorithm = lincs -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] MPI oversubscription
On Tue, Feb 5, 2013 at 8:58 AM, Berk Hess g...@hotmail.com wrote:
One last thing:
Maybe a macro is not set, but we can actually query the number of
processors.
Could you replace the conditional that gets triggered on my machine:
#if defined(_SC_NPROCESSORS_ONLN)
to
#if 1
So we can check if the actual sysconf call works or not?
My workaround won't work without OpenMP.
Did you disable that manually?
Also large file support is not turned on.
It seems like your build setup is somehow messed up and lot of features
are not found.
Could you post your CMakeFiles/CMakeError.log? That should show why those
features are disabled.
Roland
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:52:17 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
Head of .log:
Gromacs version: VERSION 5.0-dev-20121213-e1fcb0a-dirty
GIT SHA1 hash: e1fcb0a3d2768a8bb28c2e4e8012123ce773e18c (dirty)
Precision: single
MPI library: MPI
OpenMP support: disabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library: fftw-3.3.2-sse2
Large file support: disabled
RDTSCP usage: enabled
Built on: Tue Feb 5 10:58:32 CET 2013
Built by: christian@k [CMAKE]
Build OS/arch: Linux 3.4.11-2.16-desktop x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Build CPU family: 6 Model: 42 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2
ssse3 tdt
C compiler: /home/christian/opt/bin/mpicc GNU gcc (GCC) 4.8.0
20120618 (experimental)
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
-DNDEBUG
C++ compiler: /home/christian/opt/bin/mpiCC GNU g++ (GCC) 4.8.0
20120618 (experimental)
C++ compiler flags: -mavx -std=c++0x -Wextra
-Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused
-Wunused-value -Wno-unknown-pragmas -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
I will try your workaround, thanks!
2013/2/5 Berk Hess g...@hotmail.com
OK, then this is an unhandled case.
Strange, because I am also running OpenSUSE 12.2 with the same CPU, but
use gcc 4.7.1.
I will file a bug report on redmine.
Could you also post the header of md.log which gives all configuration
information?
To make it work for now, you can insert immediately after #ifdef
GMX_OMPENMP:
if (ret = 0)
{
ret = gmx_omp_get_num_procs();
}
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:27:44 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
None of the variables referenced here are set on my system, the print
statements are never executed.
What I did:
printf(Checking which processor variable is set);
#if defined(_SC_NPROCESSORS_ONLN)
ret = sysconf(_SC_NPROCESSORS_ONLN);
printf(case 1 ret = %d\n,ret);
#elif defined(_SC_NPROC_ONLN)
ret = sysconf(_SC_NPROC_ONLN);
printf(case 2 ret = %d\n,ret);
#elif defined(_SC_NPROCESSORS_CONF)
ret = sysconf(_SC_NPROCESSORS_CONF);
printf(case 3 ret = %d\n,ret);
#elif defined(_SC_NPROC_CONF)
ret = sysconf(_SC_NPROC_CONF);
printf(case 4 ret = %d\n,ret);
#endif /* End of check for sysconf argument values */
From /etc/issue:
Welcome to openSUSE 12.2 Mantis - Kernel \r (\l)
From uname -a:
Linux kafka 3.4.11-2.16-desktop #1 SMP PREEMPT Wed Sep 26 17:05:00
UTC
2012
(259fc87) x86_64 x86_64 x86_64 GNU/Linux
2013/2/5 Berk Hess g...@hotmail.com
Hi,
This is the same cpu I have in my workstation and this case should
not
cause any problems.
Which operating system and version are you using?
If you know a bit about programming, could you check what goes
wrong in
get_nthreads_hw_avail
in src/gmxlib/gmx_detect_hardware.c ?
Add after the four ret = at line 434, 436, 438 and 440:
printf(case 1 ret = %d\n,ret);
and replace 1 by different numbers.
Thus you can check if one of the 4 cases returns 0 or none of the
cases
is called.
Cheers,
Berk
Date: Tue, 5 Feb 2013 13:45:02 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
From the .log file:
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Family: 6
[gmx-users] About the Diffusion of Water Molecules
Dear Justin Thank you for your Previous reply, I am following your Protein -Lipid tutorial . I am doing simulation of Assembly of Cyclic Peptide ( Made up of Only Phenyl alanine Residue) in DPPC lipid . After I have Attained suitable APL (69 A^2) I solvated, neutralized (using genion) EMzed . Finally I Have Done NVT equilibration Using Restraint on all atoms of Lipid Molecules . At the End of My simulation I Have observed some of water molecules (60 water Molecules ) in Hydrophobic Part of Lipid Molecules (Amidst of Assembly of cyclic peptide) How to Avoid this ? Should Further Shrink APL using Perl And Then Proceeding NVT Equilibration ? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] error in running command
On 2/5/13 9:04 AM, Arunima Shilpi wrote: Dear Sir/ Madam I am using gromacs for simulation and has the following while running the command for grompp Expected integer argument for option -maxwarn . I do not want use maxwarn to bypass the error. I request you to kindly help me out to debug the error. If you don't want to use -maxwarn, then omit it from your command. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: gromacs-4.6.tar.gz installation question
Date: Mon, 04 Feb 2013 15:32:17 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] gromacs-4.6.tar.gz installation question To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 51101ad1.3000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/4/13 3:30 PM, jeela keel wrote: *Dear All, I am trying to install gromacs, I dowloaded **gromacs-4.6.tar.gzftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gzand following the instruction in the following website http://www.gromacs.org/Documentation/Installation_Instructions#4._Doing_a_build_of_GROMACS I read the instraction but I am still kind of confused. Do I need to download both FFTW and CMake or just choose one of them for the gromacs installation? Both. FFTW is used for Fourier transforms. CMake is the compiler that builds the software. Also can I use FTTW **fftw-2.1.5.tar.gzftp://ftp.fftw.org/pub/fftw/fftw-2.1.5.tar.gzinstead of **fftw-3.3.3.tar.gz ftp://ftp.fftw.org/pub/fftw/fftw-3.3.3.tar.gz becuase I also want to download Lammps in my computer that can only use fftw 2.1.5 We always advise using the newest version. There is no problem at all in maintaining different versions in different locations. In Gromacs-4.6 we have dropped support for fftw-2, which is legacy for nearly 13 years now, so you will need to install fftw-3 and btw. lammps supports fftw3 since Aug 2011. An alternative is to use gromacs build-in fftw (GMX_BUILD_OWN_FFTW=ON). Christoph -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] solvation shells
g_select can do it. E.g.: g_select -f out.gro -s topol.tpr -n index.ndx -select 'solvation_shell resname SOL and within 0.4 of group SOLUTE' -on shell.ndx might work Javier El 05/02/13 18:54, Dr. Vitaly Chaban escribió: Could anyone please remind me the name of the utility, which generates an index file for the first solvation shell, based on the distance criterion? There should be one... -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] About the Diffusion of Water Molecules
On 2/5/13 10:44 AM, vidhya sankar wrote: Dear Justin Thank you for your Previous reply, I am following your Protein -Lipid tutorial . I am doing simulation of Assembly of Cyclic Peptide ( Made up of Only Phenyl alanine Residue) in DPPC lipid . After I have Attained suitable APL (69 A^2) I solvated, neutralized (using genion) EMzed . Finally I Have Done NVT equilibration Using Restraint on all atoms of Lipid Molecules . At the End of My simulation I Have observed some of water molecules (60 water Molecules ) in Hydrophobic Part of Lipid Molecules (Amidst of Assembly of cyclic peptide) How to Avoid this ? Should Further Shrink APL using Perl And Then Proceeding NVT Equilibration ? It doesn't make any sense to me to restrain all atoms of the lipids. I would, at minimum, run NVT with no restraints on the lipids, and perhaps add a vertical restraint on water O atoms to prevent them from leaking into the membrane during the initial equilibration. Then equilibrate again for a longer time with no restraints on either water or lipids. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Translating my system using editconf causes my run to crash!
On Tue, Feb 5, 2013 at 10:05 PM, S. Alireza Bagherzadeh s.a.bagherzade...@gmail.com wrote: Hi everyone, I am using editconf to translate my system along the z-axis. Why? mdrun doesn't care. However, by trial and error I realized that only at some values of the z-component of the translation vector I am able to run my system, otherwise my run produces a number of stepN.pdb files with the following output: - Getting Loaded... Reading file topol.tpr, VERSION 4.5.5 (single precision) Loaded with Money Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1# Wrote pdb files with previous and current coordinates starting mdrun 'Methane hydrate between 2 silica surfaces in contact with water and gas' 50 steps,500.0 ps. Shake did not converge in 1000 steps Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2# Wrote pdb files with previous and current coordinates step 0Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates step 100, will finish Thu Feb 7 12:49:37 2013Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates ... [So, I do Ctrl+C to break the run] Received the INT signal, stopping at the next NS step Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates step 300, will finish Thu Feb 7 13:12:45 2013Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates Shake did not converge in 1000 steps Wrote pdb files with previous and current coordinates step 310, will finish Thu Feb 7 13:16:46 2013 NODE (s) Real (s) (%) Time:104.820106.221 98.7 1:44 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 21.511 1.739 0.256 93.623 I am using this command: editconf -f conf.gro -translate 0 0 Vz -o conf-translated.gro if Vz = 5, 10 or 35 - no error! if Vz = 15, 20, 25 or 35 - error! I have 58883 atoms in my conf.gro file with the following simulation box: 3.60900 6.60800 28.64862 This looks so strange to me! Why just translating over the z-axis causes any problem in my system??!!! Have you ever had this experience with gormacs? Would you have an insight on why this is happening? The usual reasons include 1) The system is not close to equilibrium, and the new coordinates lead to slightly different floating-point arithmetic and chaos sometimes leads to integration failure 2) You're combining the translated system with something else and overlaying atoms 3) Your .mdp file refers to something specific about the coordinate system that no longer makes sense 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: rectify the charges
Again I will remind you to keep all Gromacs-related correspondence on the gmx-users list. I am CC'ing the list and expect that all future questions and discussion will be posted there. On 2/5/13 9:52 PM, Arunima Shilpi wrote: Hello sir I would like to know how do we rectify the charges of the atom in .itp file. I did refer the manual but was unsuccessful . Here I am forwarding you the .itp file file. The manual does not contain how-to information for dealing with all possible force fields. You will have to spend considerable time in the literature reading about the force field you have chosen, how it was derived, and how you can extend it with some arbitrary molecule. Without context, there is little to suggest. It appears the output below is from PRODRG and thus you are dealing with some parameter set within the Gromos96 force field family. Consider the following: http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DRG OXT 1 -0.704 15.9994 2 C 1 DRG C 1 0.390 12.0110 3OM 1 DRG O1 -0.704 15.9994 4 CH1 1 DRG CA 10.172 13.0190 5NL 1 DRG N 10.694 14.0067 6 H 1 DRG H3 10.004 1.0080 7 H 1 DRG H4 10.004 1.0080 8 H 1 DRG H1 10.004 1.0080 9 CH2 1 DRG CB 10.140 14.0270 10 CH2 1 DRG CAT 2 -0.010 14.0270 11 S 1 DRG SAS 20.010 32.0600 12 CH2 1 DRG CAR 30.107 14.0270 13 CH1 1 DRG CAE 30.206 13.0190 14OA 1 DRG OAD 3 -0.214 15.9994 15 CH1 1 DRG CAA 30.134 13.0190 16OA 1 DRG OAG 3 -0.225 15.9994 17 H 1 DRG HAG30.041 1.0080 18 CH1 1 DRG CAB30.134 13.0190 19OA 1 DRG OAF 3 -0.225 15.9994 20 H 1 DRG HAF 30.042 1.0080 21 CH1 1 DRG CAC 40.487 13.0190 22NR 1 DRG N9 40.461 14.0067 23 CR1 1 DRG C8 4 -0.003 12.0110 24HC 1 DRG H8 40.055 1.0080 25NR 1 DRG N7 5 -0.541 14.0067 26 C 1 DRG C5 50.127 12.0110 27 C 1 DRG C450.252 12.0110 28NR 1 DRG N35 -0.556 14.0067 29 CR1 1 DRG C25 -0.004 12.0110 30HC 1 DRG H2 50.026 1.0080 31NR 1 DRG N1 5 -0.556 14.0067 32 C 1 DRG C6 50.252 12.0110 33NT 1 DRG N6 60.000 14.0067 34 H 1 DRG H62 60.000 1.0080 35 H 1 DRG H61 60.000 1.0080 *From:* Justin Lemkul jalem...@vt.edu *To:* Arunima Shilpi arunima.bioinformat...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, 5 February 2013 9:15 PM *Subject:* Re: [gmx-users] error in running command On 2/5/13 9:04 AM, Arunima Shilpi wrote: Dear Sir/ Madam I am using gromacs for simulation and has the following while running the command for grompp Expected integer argument for option -maxwarn . I do not want use maxwarn to bypass the error. I request you to kindly help me out to debug the error. If you don't want to use -maxwarn, then omit it from your command. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] a question on rerun MD after computer crash
Dear All, I have run a 5 ns MD by mdrun -deffnn md-0-1 After about 1 ns the computer was out of power by accident. I tried to continue run the MD. From the on-line material there is a method mdrun -s topol.tpr -cpi state.cpt. But by the above mdrun -deffnn md-0-1, I find I got 2 cpt files, one is md-0-1.cpt, one is md-0-1-prev.cpt. In order to continue my MD, will you please suggest I use mdrun -s md-0-1.tpr -cpi md-0-1.cpt, or I use mdrun -s md-0-1.tpr -cpi md-0-1-prev.cpt? I am looking forward to getting your reply. Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] a question on rerun MD after computer crash
Hi Acoot, Better to use the following command tpbconv -s md-0-1.tpr -extend (PUT HOW LONG YOU WANT TO RUN IN ps HERE) -o OUT_PUT.tpr mdrun -s OUT_PUT.tpr -cpi md-0-1_prev.cpt You have to use your own proper naming and do not forget to put how long you should extend it in picosecond (for example if you want to extend for 4ns you should put 4000). Cheers, EB -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Acoot Brett Sent: Wednesday, 6 February 2013 3:50 PM To: Discussion list for GROMACS users Subject: [gmx-users] a question on rerun MD after computer crash Dear All, I have run a 5 ns MD by mdrun -deffnn md-0-1 After about 1 ns the computer was out of power by accident. I tried to continue run the MD. From the on-line material there is a method mdrun -s topol.tpr -cpi state.cpt. But by the above mdrun -deffnn md-0-1, I find I got 2 cpt files, one is md-0-1.cpt, one is md-0-1-prev.cpt. In order to continue my MD, will you please suggest I use mdrun -s md-0-1.tpr -cpi md-0-1.cpt, or I use mdrun -s md-0-1.tpr -cpi md-0-1-prev.cpt? I am looking forward to getting your reply. Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] a question on rerun MD after computer crash
Dear All, For the MD extension purpose by mdrun -s OUT_PUT.tpr -cpi md-0-1_prev.cpt as discussed in the following e-mail, will you please tell me the difference between md-0-1_prev.cpt and md-0-1.cpt? I want to know the difference enven minor. I am looking forward to getting your reply. Cheers, Acoot --- On Wed, 6/2/13, Emanuel Birru emanuel.bi...@monash.edu wrote: From: Emanuel Birru emanuel.bi...@monash.edu Subject: RE: [gmx-users] a question on rerun MD after computer crash To: 'Discussion list for GROMACS users' gmx-users@gromacs.org Received: Wednesday, 6 February, 2013, 4:01 PM Hi Acoot, Better to use the following command tpbconv -s md-0-1.tpr -extend (PUT HOW LONG YOU WANT TO RUN IN ps HERE) -o OUT_PUT.tpr mdrun -s OUT_PUT.tpr -cpi md-0-1_prev.cpt You have to use your own proper naming and do not forget to put how long you should extend it in picosecond (for example if you want to extend for 4ns you should put 4000). Cheers, EB -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Acoot Brett Sent: Wednesday, 6 February 2013 3:50 PM To: Discussion list for GROMACS users Subject: [gmx-users] a question on rerun MD after computer crash Dear All, I have run a 5 ns MD by mdrun -deffnn md-0-1 After about 1 ns the computer was out of power by accident. I tried to continue run the MD. From the on-line material there is a method mdrun -s topol.tpr -cpi state.cpt. But by the above mdrun -deffnn md-0-1, I find I got 2 cpt files, one is md-0-1.cpt, one is md-0-1-prev.cpt. In order to continue my MD, will you please suggest I use mdrun -s md-0-1.tpr -cpi md-0-1.cpt, or I use mdrun -s md-0-1.tpr -cpi md-0-1-prev.cpt? I am looking forward to getting your reply. Cheers, Acoot -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] reg minimization problem
Dear sir, i have running new molecules add in standard protein that new is morin molecules unfortunetly 102 error occur which is no defualt angle found , etc. i overcome this problem but one more new appear which is shown below could you help me to overcome these following errror 26 atoms are not part of any of the T-Coupling groups can you tell what is the necessary steps carry to overcome this mistake with regards S. BOopathi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
