Re: [gmx-users] TFE-water simulation
Hello again, That depends on the peptide. There is no general answer. I am starting with a linear conformations, but that's because I'm working with intrinsically disordered proteins. That's as far as I can go regarding telling you about what I'm doing. I'm not at liberty to discuss these things, it's not public yet, sorry. Best regards, João On Fri, Nov 8, 2013 at 11:32 AM, Archana Sonawani-Jagtap ask.arch...@gmail.com wrote: Should I start with helical peptides and see if it maintains the helicity or I can start with random coil? Do random coil peptides take long simulation time to form helical peptides? any help on this will be appreciated. On Tue, Nov 5, 2013 at 12:25 AM, Archana Sonawani-Jagtap ask.arch...@gmail.com wrote: Thanks Joao Henriques for helping me with the steps. On Nov 4, 2013 3:18 PM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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
Re: [gmx-users] TFE-water simulation
Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] TFE-water simulation
Erratum: Where I wrote I ended up going with the former it should be I ended up going with the latter. /J On Mon, Nov 4, 2013 at 10:47 AM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Conversion of nm to Å
OP, I give you 10/10. First time I laugh out loud reading the GMX mailing list. /J On Wed, Aug 21, 2013 at 5:05 AM, Arunima Shilpi writetoas...@gmail.comwrote: Dear Sir I have to query as to how do we convert the paramaters in nm to Å --. For example the RMSD and RMSF calculation gives result in nm. I want to convert it to Å. I request you to kindly guide me with the process Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 -- João Henriques -- 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] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration
Thank you very much for both contributions. I will conduct some tests to assess which approach works best for my system. Much appreciated, Best regards, João Henriques On Tue, Jun 4, 2013 at 6:30 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: mdrun is not blind, just the current design does report the hardware of all compute nodes used. Whatever CPU/GPU hardware mdrun reports in the log/std output is *only* what rank 0, i.e. the first MPI process, detects. If you have a heterogeneous hardware configuration, in most cases you should be able to run just fine, but you'll still get only the hardware the first rank sits on reported. Hence, if you want to run on 5 of the nodes you mention, you just do: mpirun -np 10 mdrun_mpi [-gpu_id 01] You may want to try both -ntomp 8 and -ntomp 16 (using HyperThreading does not always help). Also note that if you use GPU sharing among ranks (in order to use 8 threads/rank), (for some technical reasons) disabling dynamic load balancing may help - especially if you have a homogenous simulation system (and hardware setup). Cheers, -- Szilárd On Tue, Jun 4, 2013 at 3:31 PM, João Henriques joao.henriques.32...@gmail.com wrote: Dear all, Since gmx-4.6 came out, I've been particularly interested in taking advantage of the native GPU acceleration for my simulations. Luckily, I have access to a cluster with the following specs PER NODE: CPU 2 E5-2650 (2.0 Ghz, 8-core) GPU 2 Nvidia K20 I've become quite familiar with the heterogenous parallelization and multiple MPI ranks per GPU schemes on a SINGLE NODE. Everything works fine, no problems at all. Currently, I'm working with a nasty system comprising 608159 tip3p water molecules and it would really help to accelerate things up a bit. Therefore, I would really like to try to parallelize my system over multiple nodes and keep the GPU acceleration. I've tried many different command combinations, but mdrun seems to be blind towards the GPUs existing on other nodes. It always finds GPUs #0 and #1 on the first node and tries to fit everything into these, completely disregarding the existence of the other GPUs on the remaining requested nodes. Once again, note that all nodes have exactly the same specs. Literature on the official gmx website is not, well... you know... in-depth and I would really appreciate if someone could shed some light into this subject. Thank you, Best regards, -- João Henriques -- 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 -- João Henriques -- 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] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration
Sorry to keep bugging you guys, but even after considering all you suggested and reading the bugzilla thread Mark pointed out, I'm still unable to make the simulation run over multiple nodes. *Here is a template of a simple submission over 2 nodes:* --- START --- #!/bin/sh # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # # Job name #SBATCH -J md # # No. of nodes and no. of processors per node #SBATCH -N 2 #SBATCH --exclusive # # Time needed to complete the job #SBATCH -t 48:00:00 # # Add modules module load gcc/4.6.3 module load openmpi/1.6.3/gcc/4.6.3 module load cuda/5.0 module load gromacs/4.6 # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # grompp -f md.mdp -c npt.gro -t npt.cpt -p topol -o md.tpr mpirun -np 4 mdrun_mpi -gpu_id 01 -deffnm md -v # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --- END --- *Here is an extract of the md.log:* --- START --- Using 4 MPI processes Using 4 OpenMP threads per MPI process Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz Family: 6 Model: 45 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 2 GPUs detected on host en001: #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible #1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible --- Program mdrun_mpi, VERSION 4.6 Source code file: /lunarc/sw/erik/src/gromacs/gromacs-4.6/src/gmxlib/gmx_detect_hardware.c, line: 322 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 4 PP MPI processes per node, but you provided 2 GPUs. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- --- END --- As you can see, gmx is having trouble understanding that there's a second node available. Note that since I did not specify -ntomp, it assigned 4 threads to each of the 4 mpi processes (filling the entire avail. 16 CPUs *on one node*). For the same exact submission, if I do set -ntomp 8 (since I have 4 MPI procs * 8 OpenMP threads = 32 CPUs total on the 2 nodes) I get a warning telling me that I'm hyperthreading, which can only mean that *gmx is assigning all processes to the first node once again.* Am I doing something wrong or is there some problem with gmx-4.6? I guess it can only be my fault, since I've never seen anyone else complaining about the same issue here. *Here are the cluter specs details:* http://www.lunarc.lu.se/Systems/ErikDetails Thank you for your patience and expertise, Best regards, João Henriques On Tue, Jun 4, 2013 at 6:30 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: mdrun is not blind, just the current design does report the hardware of all compute nodes used. Whatever CPU/GPU hardware mdrun reports in the log/std output is *only* what rank 0, i.e. the first MPI process, detects. If you have a heterogeneous hardware configuration, in most cases you should be able to run just fine, but you'll still get only the hardware the first rank sits on reported. Hence, if you want to run on 5 of the nodes you mention, you just do: mpirun -np 10 mdrun_mpi [-gpu_id 01] You may want to try both -ntomp 8 and -ntomp 16 (using HyperThreading does not always help). Also note that if you use GPU sharing among ranks (in order to use 8 threads/rank), (for some technical reasons) disabling dynamic load balancing may help - especially if you have a homogenous simulation system (and hardware setup). Cheers, -- Szilárd On Tue, Jun 4, 2013 at 3:31 PM, João Henriques joao.henriques.32...@gmail.com wrote: Dear all, Since gmx-4.6 came out, I've been particularly interested in taking advantage of the native GPU acceleration for my simulations. Luckily, I have access to a cluster with the following specs PER NODE: CPU 2 E5-2650 (2.0 Ghz, 8-core) GPU 2 Nvidia K20 I've become quite familiar with the heterogenous parallelization and multiple MPI ranks per GPU schemes on a SINGLE NODE. Everything works fine, no problems at all. Currently, I'm working with a nasty system comprising 608159 tip3p water molecules and it would really help to accelerate things up a bit. Therefore, I would really like to try to parallelize my system over multiple nodes and keep the GPU acceleration. I've tried many different command combinations, but mdrun seems to be blind towards the GPUs existing on other nodes. It always finds GPUs #0 and #1 on the first node and tries to fit
Re: [gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration
Ok, thanks once again. I will do my best to overcome this issue. Best regards, João Henriques On Wed, Jun 5, 2013 at 3:33 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, Jun 5, 2013 at 2:53 PM, João Henriques joao.henriques.32...@gmail.com wrote: Sorry to keep bugging you guys, but even after considering all you suggested and reading the bugzilla thread Mark pointed out, I'm still unable to make the simulation run over multiple nodes. *Here is a template of a simple submission over 2 nodes:* --- START --- #!/bin/sh # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # # Job name #SBATCH -J md # # No. of nodes and no. of processors per node #SBATCH -N 2 #SBATCH --exclusive # # Time needed to complete the job #SBATCH -t 48:00:00 # # Add modules module load gcc/4.6.3 module load openmpi/1.6.3/gcc/4.6.3 module load cuda/5.0 module load gromacs/4.6 # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # grompp -f md.mdp -c npt.gro -t npt.cpt -p topol -o md.tpr mpirun -np 4 mdrun_mpi -gpu_id 01 -deffnm md -v # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --- END --- *Here is an extract of the md.log:* --- START --- Using 4 MPI processes Using 4 OpenMP threads per MPI process Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz Family: 6 Model: 45 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 2 GPUs detected on host en001: #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible #1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible --- Program mdrun_mpi, VERSION 4.6 Source code file: /lunarc/sw/erik/src/gromacs/gromacs-4.6/src/gmxlib/gmx_detect_hardware.c, line: 322 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. per node is critical here. mdrun_mpi was started with 4 PP MPI processes per node, but you provided 2 GPUs. ...and here. As far as mdrun_mpi knows from the MPI system there's only MPI ranks on this one node. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- --- END --- As you can see, gmx is having trouble understanding that there's a second node available. Note that since I did not specify -ntomp, it assigned 4 threads to each of the 4 mpi processes (filling the entire avail. 16 CPUs *on one node*). For the same exact submission, if I do set -ntomp 8 (since I have 4 MPI procs * 8 OpenMP threads = 32 CPUs total on the 2 nodes) I get a warning telling me that I'm hyperthreading, which can only mean that *gmx is assigning all processes to the first node once again.* Am I doing something wrong or is there some problem with gmx-4.6? I guess it can only be my fault, since I've never seen anyone else complaining about the same issue here. Assigning MPI processes to nodes is a matter configuring your MPI. GROMACS just follows the MPI system information it gets from MPI - hence the oversubscription. If you assign two MPI processes to each node, then things should work. 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 -- João Henriques -- 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] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration
Just to wrap up this thread, it does work when the mpirun is properly configured. I knew it had to be my fault :) Something like this works like a charm: mpirun -npernode 2 mdrun_mpi -ntomp 8 -gpu_id 01 -deffnm md -v Thank you Mark and Szilárd for your invaluable expertise. Best regards, João Henriques On Wed, Jun 5, 2013 at 4:21 PM, João Henriques joao.henriques.32...@gmail.com wrote: Ok, thanks once again. I will do my best to overcome this issue. Best regards, João Henriques On Wed, Jun 5, 2013 at 3:33 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, Jun 5, 2013 at 2:53 PM, João Henriques joao.henriques.32...@gmail.com wrote: Sorry to keep bugging you guys, but even after considering all you suggested and reading the bugzilla thread Mark pointed out, I'm still unable to make the simulation run over multiple nodes. *Here is a template of a simple submission over 2 nodes:* --- START --- #!/bin/sh # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # # Job name #SBATCH -J md # # No. of nodes and no. of processors per node #SBATCH -N 2 #SBATCH --exclusive # # Time needed to complete the job #SBATCH -t 48:00:00 # # Add modules module load gcc/4.6.3 module load openmpi/1.6.3/gcc/4.6.3 module load cuda/5.0 module load gromacs/4.6 # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # grompp -f md.mdp -c npt.gro -t npt.cpt -p topol -o md.tpr mpirun -np 4 mdrun_mpi -gpu_id 01 -deffnm md -v # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --- END --- *Here is an extract of the md.log:* --- START --- Using 4 MPI processes Using 4 OpenMP threads per MPI process Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz Family: 6 Model: 45 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 2 GPUs detected on host en001: #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible #1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible --- Program mdrun_mpi, VERSION 4.6 Source code file: /lunarc/sw/erik/src/gromacs/gromacs-4.6/src/gmxlib/gmx_detect_hardware.c, line: 322 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. per node is critical here. mdrun_mpi was started with 4 PP MPI processes per node, but you provided 2 GPUs. ...and here. As far as mdrun_mpi knows from the MPI system there's only MPI ranks on this one node. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- --- END --- As you can see, gmx is having trouble understanding that there's a second node available. Note that since I did not specify -ntomp, it assigned 4 threads to each of the 4 mpi processes (filling the entire avail. 16 CPUs *on one node*). For the same exact submission, if I do set -ntomp 8 (since I have 4 MPI procs * 8 OpenMP threads = 32 CPUs total on the 2 nodes) I get a warning telling me that I'm hyperthreading, which can only mean that *gmx is assigning all processes to the first node once again.* Am I doing something wrong or is there some problem with gmx-4.6? I guess it can only be my fault, since I've never seen anyone else complaining about the same issue here. Assigning MPI processes to nodes is a matter configuring your MPI. GROMACS just follows the MPI system information it gets from MPI - hence the oversubscription. If you assign two MPI processes to each node, then things should work. 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 -- João Henriques -- João Henriques -- 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] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration
Dear all, Since gmx-4.6 came out, I've been particularly interested in taking advantage of the native GPU acceleration for my simulations. Luckily, I have access to a cluster with the following specs PER NODE: CPU 2 E5-2650 (2.0 Ghz, 8-core) GPU 2 Nvidia K20 I've become quite familiar with the heterogenous parallelization and multiple MPI ranks per GPU schemes on a SINGLE NODE. Everything works fine, no problems at all. Currently, I'm working with a nasty system comprising 608159 tip3p water molecules and it would really help to accelerate things up a bit. Therefore, I would really like to try to parallelize my system over multiple nodes and keep the GPU acceleration. I've tried many different command combinations, but mdrun seems to be blind towards the GPUs existing on other nodes. It always finds GPUs #0 and #1 on the first node and tries to fit everything into these, completely disregarding the existence of the other GPUs on the remaining requested nodes. Once again, note that all nodes have exactly the same specs. Literature on the official gmx website is not, well... you know... in-depth and I would really appreciate if someone could shed some light into this subject. Thank you, Best regards, -- João Henriques -- 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] Restarting a REMD simulation (error)
Dear all, Due to cluster wall-time limitations, I was forced to restart two REMD simulations. It ran absolutely fine until hitting the wall-time. To restart I used the following command: mpirun -np 64 -output-filename MPIoutput $GromDir/mdrun_mpi -s H5_.tpr -multi 64 -replex 1000 -deffnm H5_ -cpi -noappend (I'm using GMX-4.0.7 and yes I know it's old but I have my own reasons for using it.) Here is a random replica (#1) MPI output: ##START### NNODES=64, MYRANK=1, HOSTNAME=an091 NODEID=1 argc=11 Checkpoint file is from part 1, new output files will be suffixed part0002. Reading file H5_1.tpr, VERSION 4.0.7 (single precision) Reading checkpoint file H5_1.cpt generated: Wed Apr 3 17:13:14 2013 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: main.c, line: 116 Fatal error: The 64 subsystems are not compatible --- Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 1 out of 64 ##END### It's reading from the correct cpt and tpr files, so it must be something else. Here is a tail of the respective log file: ##START### Initializing Replica Exchange Repl There are 64 replicas: Multi-checking the number of atoms ... OK Multi-checking the integrator ... OK Multi-checking init_step+nsteps ... OK Multi-checking first exchange step: init_step/-replex ... first exchange step: init_step/-replex is not equal for all subsystems subsystem 0: 3062 subsystem 1: 3062 subsystem 2: 3062 subsystem 3: 3062 subsystem 4: 3062 subsystem 5: 3062 subsystem 6: 3062 subsystem 7: 3062 subsystem 8: 3062 subsystem 9: 3062 subsystem 10: 3062 subsystem 11: 3062 subsystem 12: 3062 subsystem 13: 3062 subsystem 14: 3062 subsystem 15: 3062 subsystem 16: 3062 subsystem 17: 3062 subsystem 18: 3062 subsystem 19: 3062 subsystem 20: 3062 subsystem 21: 3062 subsystem 22: 3062 subsystem 23: 3062 subsystem 24: 3062 subsystem 25: 3062 subsystem 26: 3062 subsystem 27: 3062 subsystem 28: 3062 subsystem 29: 3062 subsystem 30: 3062 subsystem 31: 3062 subsystem 32: 3062 subsystem 33: 3062 subsystem 34: 3062 subsystem 35: 3062 subsystem 36: 3062 subsystem 37: 3062 subsystem 38: 3062 subsystem 39: 3066 subsystem 40: 3062 subsystem 41: 3062 subsystem 42: 3062 subsystem 43: 3062 subsystem 44: 3062 subsystem 45: 3062 subsystem 46: 3062 subsystem 47: 3062 subsystem 48: 3062 subsystem 49: 3062 subsystem 50: 3062 subsystem 51: 3062 subsystem 52: 3062 subsystem 53: 3062 subsystem 54: 3062 subsystem 55: 3062 subsystem 56: 3062 subsystem 57: 3062 subsystem 58: 3062 subsystem 59: 3062 subsystem 60: 3062 subsystem 61: 3062 subsystem 62: 3062 subsystem 63: 3062 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: main.c, line: 116 Fatal error: The 64 subsystems are not compatible --- ##END### It's clear that init_step/-replex is not equal for all subsystems is the problem, but does anyone know why this is happening and how to solve it? Thank you for your patience, Best regards, João Henriques -- 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] Restarting a REMD simulation (error)
Thank you very much. I didn't notice it until now considering all those numbers look so similar. Great eye for detail! João On Mon, Apr 8, 2013 at 3:17 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Apr 8, 2013 8:53 AM, João Henriques joao.henriques.32...@gmail.com wrote: Dear all, Due to cluster wall-time limitations, I was forced to restart two REMD simulations. It ran absolutely fine until hitting the wall-time. To restart I used the following command: mpirun -np 64 -output-filename MPIoutput $GromDir/mdrun_mpi -s H5_.tpr -multi 64 -replex 1000 -deffnm H5_ -cpi -noappend (I'm using GMX-4.0.7 and yes I know it's old but I have my own reasons for using it.) Here is a random replica (#1) MPI output: ##START### NNODES=64, MYRANK=1, HOSTNAME=an091 NODEID=1 argc=11 Checkpoint file is from part 1, new output files will be suffixed part0002. Reading file H5_1.tpr, VERSION 4.0.7 (single precision) Reading checkpoint file H5_1.cpt generated: Wed Apr 3 17:13:14 2013 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: main.c, line: 116 Fatal error: The 64 subsystems are not compatible --- Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 1 out of 64 ##END### It's reading from the correct cpt and tpr files, so it must be something else. Here is a tail of the respective log file: ##START### Initializing Replica Exchange Repl There are 64 replicas: Multi-checking the number of atoms ... OK Multi-checking the integrator ... OK Multi-checking init_step+nsteps ... OK Multi-checking first exchange step: init_step/-replex ... first exchange step: init_step/-replex is not equal for all subsystems subsystem 0: 3062 subsystem 1: 3062 subsystem 2: 3062 subsystem 3: 3062 subsystem 4: 3062 subsystem 5: 3062 subsystem 6: 3062 subsystem 7: 3062 subsystem 8: 3062 subsystem 9: 3062 subsystem 10: 3062 subsystem 11: 3062 subsystem 12: 3062 subsystem 13: 3062 subsystem 14: 3062 subsystem 15: 3062 subsystem 16: 3062 subsystem 17: 3062 subsystem 18: 3062 subsystem 19: 3062 subsystem 20: 3062 subsystem 21: 3062 subsystem 22: 3062 subsystem 23: 3062 subsystem 24: 3062 subsystem 25: 3062 subsystem 26: 3062 subsystem 27: 3062 subsystem 28: 3062 subsystem 29: 3062 subsystem 30: 3062 subsystem 31: 3062 subsystem 32: 3062 subsystem 33: 3062 subsystem 34: 3062 subsystem 35: 3062 subsystem 36: 3062 subsystem 37: 3062 subsystem 38: 3062 subsystem 39: 3066 Seems system 39 got its IO done faster. Its state_prev.cpt will be 3062. Back up your files. Use gmxcheck to see what's in files. Rename as suitable so your set of files is consistent. Mark subsystem 40: 3062 subsystem 41: 3062 subsystem 42: 3062 subsystem 43: 3062 subsystem 44: 3062 subsystem 45: 3062 subsystem 46: 3062 subsystem 47: 3062 subsystem 48: 3062 subsystem 49: 3062 subsystem 50: 3062 subsystem 51: 3062 subsystem 52: 3062 subsystem 53: 3062 subsystem 54: 3062 subsystem 55: 3062 subsystem 56: 3062 subsystem 57: 3062 subsystem 58: 3062 subsystem 59: 3062 subsystem 60: 3062 subsystem 61: 3062 subsystem 62: 3062 subsystem 63: 3062 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: main.c, line: 116 Fatal error: The 64 subsystems are not compatible --- ##END### It's clear that init_step/-replex is not equal for all subsystems is the problem, but does anyone know why this is happening and how to solve it? Thank you for your patience, Best regards, João Henriques -- 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 -- João Henriques -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive
Re: [gmx-users] replica exchange data in cpt file
Thank you Mark and Francesco. I will be pleased to contribute with a fix in case I come up with a fairly general solution for this issue. Best regards, João Henriques On Thu, Apr 4, 2013 at 7:45 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Demux.pl pre-dates .cpt and -append. The only solution is to preserve your .log files (e.g. with -noappend) and post-process. If you do that by modifying demux.pl, please consider contributing your fix back. Mark On Apr 4, 2013 1:42 PM, francesco oteri francesco.ot...@gmail.com wrote: if your -append option is activated (the default is yes), maybe Demux.pl reads the exchanging from the .log taking into account the time in the log and so you don't need to do anything. But I don't know how Demux.pl works :( Francesco 2013/4/4 João Henriques joao.henriques.32...@gmail.com That's terrible! I was just about to restart 2 hefty REMD simulations... Maybe I can move the original log files somewhere and combine them with the restart ones afterwards by using a script. It's just an idea, because I need to run Demux.pl on the final concatenated log file. Any other issues I should be aware of? Best regards, João Henriques On Thu, Apr 4, 2013 at 12:18 PM, francesco oteri francesco.ot...@gmail.comwrote: This is what I meant, in particular it is a problem when I want to analyze the data regarding the exchange probability. Francesco 2013/4/4 João Henriques joao.henriques.32...@gmail.com So let me see if I understood what Francesco said correctly. Restarting a REMD job after hitting the cluster wall-time limit resets the information stored in the log files? Can someone shed some light on this subject? Best regards, João Henriques -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 -- João Henriques -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 -- João Henriques -- 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] replica exchange data in cpt file
So let me see if I understood what Francesco said correctly. Restarting a REMD job after hitting the cluster wall-time limit resets the information stored in the log files? Can someone shed some light on this subject? Best regards, João Henriques -- 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] replica exchange data in cpt file
That's terrible! I was just about to restart 2 hefty REMD simulations... Maybe I can move the original log files somewhere and combine them with the restart ones afterwards by using a script. It's just an idea, because I need to run Demux.pl on the final concatenated log file. Any other issues I should be aware of? Best regards, João Henriques On Thu, Apr 4, 2013 at 12:18 PM, francesco oteri francesco.ot...@gmail.comwrote: This is what I meant, in particular it is a problem when I want to analyze the data regarding the exchange probability. Francesco 2013/4/4 João Henriques joao.henriques.32...@gmail.com So let me see if I understood what Francesco said correctly. Restarting a REMD job after hitting the cluster wall-time limit resets the information stored in the log files? Can someone shed some light on this subject? Best regards, João Henriques -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 -- João Henriques -- 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] do_dssp Segmentation fault
Hello, do_dssp (4.5.5) is broken. There are two possible answers you're gonna get here: 1) Use old dssp, which you are using. 2) You're an idiot, which are not. What I did to solve the problem was, download gmx from git, and substitute the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the git version. Re-compile it and voila! This do_dssp version accepts both old and new dssp and you have to specify which version with the flag -ver if I remember correctly. This worked perfectly for me. I hope it helps you as well. All the best, João Henriques On Mon, Nov 12, 2012 at 8:38 AM, mshappy1986 mshappy1...@126.com wrote: Hi all, I am meeting the following error in Gromacs 4.5.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o dssp.xpm give me the following error segmentation fault I have downloaded the executable DSSP form http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but do_dssp did not work. How can I fix it? Thanks a lot -- 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 -- João Henriques -- 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] dssp and gromacs version
Gromacs' 4.5.5 do_dssp is broken. There is a patch for it in git. I haven't tried it out, so I can't say for sure it works. This is not a DSSP problem, it's a Gromacs problem. Just to reinforce the idea, the new DSSP should not be used, no matter which Gromacs version you're using. Best regards, Joao Henriques On Fri, Mar 2, 2012 at 9:10 AM, lina lina.lastn...@gmail.com wrote: On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 2/03/2012 6:52 PM, lina wrote: Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, The new DSSP is not compatible with any GROMACS Ha ... the dssp complain the segmentation fault in 4.5.5, but can run smoothly in 4.5.3. IIRC, seems there were some threads talked about that before. 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 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 -- João Henriques -- 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: Antw: Re: Re: [gmx-users] constant PH simulations
There is no problem in being wrong. The problem is that he wants to be wrong. At least 4 different researchers gave constructive input and this subject keeps hitting the same key. I've always been told that worse than not knowing, is not wanting to know. Still, I apologize for my outburst. Best regards, On Wed, Sep 7, 2011 at 1:54 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 7/09/2011 3:53 AM, João Henriques wrote: I guess someone has been living in a cave for the past decade or so... Please keep contributions to the mailing list constructive :-) Everyone's been wrong before! Mark -- 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 -- João Henriques -- 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: Re: Antw: Re: Re: [gmx-users] constant PH simulations
Why don't you read the papers associated with the link everyone keeps sending you!!! Stop it with the autistic behavior. http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Here is the main paper regarding the CpH-MD method I'm currently using: http://jcp.aip.org/resource/1/jcpsa6/v117/i9/p4184_s1 Here's a tip: searching google scholar a little before emailing everyone in the list should prove useful. Cheers, On Wed, Sep 7, 2011 at 11:01 AM, Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de wrote: At first I would like to say that I deeply apologize for the cave-like things I have said. I again say, that this was not the field I am deeply involved. From Gerrit I got a banana. For this guy, I am a cave-man. Thanks, for being such ready for open discussion. I did not tell that I do not want to be wrong. Questions, which are included in my doubts: Generalized forces and averages for H+ interchange ? Comparison with titration experiments ? Is there any experimental evidence for the rates of interchange ? Are simulation-times or the periods of interchange at any time realistic? Are equilibria sampled well, with such interchanges, or are there jumps in free energy by this interchange ? Why is there no free H+ ? Thanks for your kind and very constructive criticisms. I would appreciate, if this so-called discussion will find an end. I am deeply depressed about such comments and I will not take part in any users-discussion in the future. It makes no sense, because talking like this expresses the way on how science is done today. Repelling that person, who does not walk the common way. And: Maybe I have lived in a cave, but someone like you, who answers in such a way, IS A CAVEMAN ! João Henriquesjoao.henriques.32...@gmail.com 07.09.11 11.30 Uhr There is no problem in being wrong. The problem is that he wants to be wrong. At least 4 different researchers gave constructive input and this subject keeps hitting the same key. I've always been told that worse than not knowing, is not wanting to know. Still, I apologize for my outburst. Best regards, On Wed, Sep 7, 2011 at 1:54 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 7/09/2011 3:53 AM, João Henriques wrote: I guess someone has been living in a cave for the past decade or so... Please keep contributions to the mailing list constructive :-) Everyone's been wrong before! Mark -- 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 -- João Henriques -- 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 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 -- João Henriques -- 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: Antw: Re: Re: [gmx-users] constant PH simulations
No forcefield on whole earth is able to reproduce the pH realistically by H+. You just can apply pH of your system through the protonation states of each part in your system. I guess someone has been living in a cave for the past decade or so... Cheers, -- João Henriques -- 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] Changing the pH
Hi Tanos, Perhaps you should try one of the available constant-pH MD methods. Here is a quick explanation of what they do and who is involved in their development right now: http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation My opinion regarding this subject may be a little biased since I've worked with one of the most active researchers in this area, but I would suggest you to read some papers from Antonio Baptista and/or Miguel Machuqueiro (from Baptista's 2002 initial Constant-pH molecular dynamics using stochastic titration paper to nowadays). Best regards, On Tue, May 10, 2011 at 7:22 AM, Justin A. Lemkul jalem...@vt.edu wrote: Tanos Celmar Costa Franca wrote: Dear GROMACS users, Does someone now how to procede to change the pH of a MD simulation from the physiologic one (7.4) to 6.5 ? Classical MD simulations do not currently allow for dynamic proton exchange. The best you can do at the moment is use pdb2gmx to set the protonation state of titratable residues. At pH 6.5, histidines will be quite annoying to deal with properly. -Justin Tanos Celmar Costa Franca - D.Sc Coordenador do Programa de Pos-graduacão em Química Secão de Engenharia Química - SE/5 Instituto Militar de Engenharia - IME Rio de Janeiro - RJ Brasil This message was sent using IMP, the Internet Messaging Program. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- João Henriques, MSc in Biochemistry Faculty of Science of the University of Lisbon Department of Chemistry and Biochemistry C8 Building, Room 8.5.47 Campo Grande, 1749-016 Lisbon, Portugal E-mail: joao.henriques.32...@gmail.com / jmhenriq...@fc.ul.pt http://intheochem.fc.ul.pt/members/joaoh.html -- 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] Adding water to protein to start the simulation process
With all due respect, this is clearly a RT*M moment. * = F Joao Henriques On Fri, Apr 15, 2011 at 1:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Monisha Hajra wrote: Hi Justin, I am trying to follow the protocol only. More than the Gromacs own website, I find http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is more useful. Clearly. This is one of many tutorials linked from the site I posted before. However, I am stuck at one step which is mentioned : http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html I am not able to understand how to create traj.trr, traj.xtc and ener.edr file. Remaining all is self explained in the previous link. These files are output by mdrun, i.e. actually running a simulation. -Justin Really appreciate any help. Regards Monisha On Fri, Apr 15, 2011 at 8:06 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Monisha Hajra wrote: Hi User, I have a protein which I have modeled by Homology modelling. The modeled protein has no water molecules in its surrounding environment. How should I add water molecule so that I can start the simulation process? Please refer to the abundant tutorial material on the website: http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation -Justin Regards Monisha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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
