[gmx-users] GPU problem
Dear: I've got four GPU in one workstation. I am trying to run two GPU job with command: mdrun -s md.tpr -gpu_id 01 mdrun -s md.tpr -gpu_id 23 there are 32 CPU in this workstation. I found that each job trying to use the whole CPU, and there are 64 sub job when these two GPU mdrun submitted. Moreover, one of the job stopped after short of running, probably because of the CPU issue. I am just wondering, how can we distribute CPU when we run two GPU job in a single workstation? thank you very much best Albert -- 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] problem using g_lie
hii I ran a protein ligand simulation and only ligand simualtion in water using GROMACS 4.5.4 I want to find the binding energy of the ligand and used g_lie. I tried to run g_lie on ligand simulation in water and got the following result Opened md_1.edr as single precision energy file Using the following energy terms: LJ: Coul: Back Off! I just backed up lie.xvg to ./#lie.xvg.3# Last energy frame read 2500 time 5000.000 DGbind = -0.681 (-nan) Can anyone tell me what is the problem and how to go about with this -- 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] GPU problem
Hi Albert, I think using -nt flag (-nt=16) with mdrun would solve your problem. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Jun 4, 2013 at 12:56 PM, Albert mailmd2...@gmail.com wrote: Dear: I've got four GPU in one workstation. I am trying to run two GPU job with command: mdrun -s md.tpr -gpu_id 01 mdrun -s md.tpr -gpu_id 23 there are 32 CPU in this workstation. I found that each job trying to use the whole CPU, and there are 64 sub job when these two GPU mdrun submitted. Moreover, one of the job stopped after short of running, probably because of the CPU issue. I am just wondering, how can we distribute CPU when we run two GPU job in a single workstation? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] REMD run showing temperature range more than the equilibrated.
Hi all ! well, I'm working on REMD with 96 replicas, with temperature range 280K to 425.04K. The NVT equilibration works well and graphs plotted show almost the required temperature after equilibration. Then, after 3 ns of remd run , the edr - xvg files show initial temperature atleast 40 -50 units up , and then gradually reduces to it's temperature. for example replica 0 has 280 temperature , for initial 40 ps, it shows temperature up till 335K an then, decline. and around 21st to 22nd replica, the exchange probability is varying a lot from 20% to 60%. so, my queries are how to resolve this temperature issue and why is the exchange probability so abrupt at 21-22 replica ? Thanks -- 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 Physaica Parameter
On 6/4/13 5:06 AM, vidhya sankar wrote: Dear Justin Mark Thank you for your previous reply I am doing Simulation of CNT wrapped By Cyclic Peptide in Water For that I have used the Parameters as follows for my production run ns_type= grid nstlist= 5 rlist= 1.8 rcoulomb= 1.2 vdwtype = Shift rvdw= 1.2 coulombtype= Reaction-Field-zero pme_order= 4 fourierspacing= 0.16 pcoupl= Parrinello-Rahman pcoupltype= semiisotropic (Because My system is Composed of both pure Hydrophobic(CNT) Hydrophilic IProtein) part and Immersed in water) tau_p= 2.0 ref_p= 1.01.0 compressibility = 4.5e-54.5e-5 It run well But How to check is all these parameters are wright or wrong? Is Theer is Any thumb rule to Assign parameters ? The cutoffs look bizarre. They should be set based on the parent force field. Because My system is Composed of both pure Hydrophobic(CNT) Hydrophilic IProtein) part and Immersed in water so I have Selected semiisotropic That does not make sense. Semiisotropic coupling is for systems that deform in x-y and z independently, not due to the chemical nature of the molecules in the system. What are the parameters Should i Concentrate and How to choose its value carefully rationally ? Base your settings on a thorough understanding of your chosen force field and an examination of the literature for other algorithms to understand their benefits and limitations. -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] problem using g_lie
On 6/4/13 3:56 AM, khushboo bafna wrote: hii I ran a protein ligand simulation and only ligand simualtion in water using GROMACS 4.5.4 I want to find the binding energy of the ligand and used g_lie. I tried to run g_lie on ligand simulation in water and got the following result Opened md_1.edr as single precision energy file Using the following energy terms: LJ: Coul: Back Off! I just backed up lie.xvg to ./#lie.xvg.3# Last energy frame read 2500 time 5000.000 DGbind = -0.681 (-nan) Can anyone tell me what is the problem and how to go about with this To use g_lie, you need to be analyzing an .edr file that comes from the protein-ligand simulation, providing the values of the ligand-water interactions to -Elj and -Eqq, which are simply extracted from the ligand-water .edr using g_energy. -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] High Initial generated Temp
Dear All, Although I have set gen_temp = 300, it is showing the initial temperature 445.7 K, generated at the very beginning of the run. gen_vel = yes ; velocity generation gen_temp= 300 gen_seed= 93873959697 Is it because of a bad geometry? In mailing list I came across this thread [ http://comments.gmane.org/gmane.science.biology.gromacs.user/41931] Prior to this production run, I heated my system slowly from 0 K to 300 K within 300 ps time span. It would be very helpful if someone suggests me the way to deal with this problem? Thanks, Tarak -- 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] High Initial generated Temp
On 6/4/13 8:07 AM, tarak karmakar wrote: Dear All, Although I have set gen_temp = 300, it is showing the initial temperature 445.7 K, generated at the very beginning of the run. gen_vel = yes ; velocity generation gen_temp= 300 gen_seed= 93873959697 Is it because of a bad geometry? In mailing list I came across this thread [ http://comments.gmane.org/gmane.science.biology.gromacs.user/41931] Prior to this production run, I heated my system slowly from 0 K to 300 K within 300 ps time span. It would be very helpful if someone suggests me the way to deal with this problem? A full .mdp file is always more useful than a small snippet. I have seen this same behavior when the continuation parameter is incorrectly set - have you used continuation = yes in your .mdp file? If not, the constraints get messed up and your initial velocities can get all messed up. A larger point is this - why are you re-generating velocities after heating the system from 0 to 300 K? Why not simply preserve the ensemble at 300 K by using a .cpt file? -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] About Physical parameters
Dear Justin Thank you for your Previuos reply I am using gromos53a6 ff When i changed the parameters for cut-off (r list ) value to 1.2 I have got Error as follows What is the Meaning of Note 2 3 NOTE 2 [file cntcycpepfull2.mdp]: The switch/shift interaction settings are just for compatibility; you will get betterperformance from applying potential modifiers to your interactions! NOTE 3 [file cntcycpepfull2.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb. NOTE 4 [file cntcycpepfull2.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. WARNING 1 [file cntcycpepfull2.mdp]: The sum of the two largest charge group radii (0.518710) is larger than rlist (1.20) - rvdw (1.20) WARNING 2 [file cntcycpepfull2.mdp]: The sum of the two largest charge group radii (0.518710) is larger than rlist (1.20) - rcoulomb (1.20) nstlist= 5 rlist= 1.2 rcoulomb= 1.2 vdwtype = Shift rvdw= 1.2 coulombtype= Reaction-Field-zero pme_order= 4 fourierspacing= 0.16 pcoupl= Parrinello-Rahman pcoupltype= isotropic thus .grompp terminated due to warnings To Avoid his I have used the rlist=1.8 (in Above valuue) Because the difference betwen rlist-rcoloum should Be greater than 0.518710 But you maild me the cut-off looks Bizarre .it should be based on parent force field(mine is gromos53a6) I hope your kind Suugestion are useful to get succesfull production mdrun Thanks In ADVANCE -- 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 Physical parameters
On 6/4/13 8:22 AM, vidhya sankar wrote: Dear Justin Thank you for your Previuos reply I am using gromos53a6 ff When i changed the parameters for cut-off (r list ) value to 1.2 I have got Error as follows What is the Meaning of Note 2 3 NOTE 2 [file cntcycpepfull2.mdp]: The switch/shift interaction settings are just for compatibility; you will get betterperformance from applying potential modifiers to your interactions! NOTE 3 [file cntcycpepfull2.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb. NOTE 4 [file cntcycpepfull2.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. WARNING 1 [file cntcycpepfull2.mdp]: The sum of the two largest charge group radii (0.518710) is larger than rlist (1.20) - rvdw (1.20) WARNING 2 [file cntcycpepfull2.mdp]: The sum of the two largest charge group radii (0.518710) is larger than rlist (1.20) - rcoulomb (1.20) nstlist= 5 rlist= 1.2 rcoulomb= 1.2 vdwtype = Shift rvdw= 1.2 coulombtype= Reaction-Field-zero pme_order= 4 fourierspacing= 0.16 pcoupl= Parrinello-Rahman pcoupltype= isotropic thus .grompp terminated due to warnings To Avoid his I have used the rlist=1.8 (in Above valuue) Because the difference betwen rlist-rcoloum should Be greater than 0.518710 But you maild me the cut-off looks Bizarre .it should be based on parent force field(mine is gromos53a6) If you're using Gromos96 53A6, nearly all of your settings are wrong. Please refer to the primary literature for the force field and the many posts in the list archive regarding proper use of that force field. Making ad hoc changes just to get grompp to stop complaining is a very error-prone way to do simulations (which end up being unstable or invalid by doing so). -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] Can we connect two boxes together for the simulation?
Hi, all, I want to do NPT simulations with different compositions first. Then I want to connect the two boxes to continue the NPT simulation. I mean, after simulations, we get two boxes with different compositions. Can we do that with gromacs? or how can we do that? Thanks. Best, Kai -- 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: gmx 4.6 mpi installation through openmpi?
I received this answer: Mark Abraham Mon, 03 Jun 2013 08:02:56 -0700 That looks like there's a PGI compiler getting used at some point (perhaps the internal FFTW build is picking up the CC environment var? I forget how that gets its compiler!). If you do find * -name config.log then perhaps you can see in that file what the FFTW build thinks about its compiler. Mark I found the config.log file and checked that the compiler being used to compile the internal FFTW is the same version of gcc that is used to compile the rest of Gromacs. In fact, I set the environment variable CC to gcc. I also tried to clean and compile from scratch the FFTW, but no success. I also tried to specify with the environment variable CMAKE_LIBRARY_PATH where the FFTW library is (in my case in gromacs-4.6/src/contrib/fftw/gmxfftw-prefix/lib), but I obtained the same error. Any other idea? Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/gmx-4-6-mpi-installation-through-openmpi-tp5006975p5008782.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Performance of Gromacs-4.6.1 on BlueGene/Q
Dear All, Has anyone has Gromacs benchmark on Bluegene/Q? I recently installed gromacs-461 on BG/Q using the following command: cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \ -DGMX_BUILD_OWN_FFTW=ON \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_XML=OFF \ -DCMAKE_INSTALL_PREFIX=/scratch/home/biilijg/package/gromacs-461 make make install After that, I did a benchmark simulation using a box of pure water containing 140k atoms. The command I used for the above test is: srun --ntasks-per-node=32 --overcommit /scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c box_md1.gro -x box_md1.xtc -g md1.log job_md1 And I got the following performance: Num. cores hour/ns 128 9.860 256 4.984 512 2.706 1024 1.544 2048 0.978 4092 0.677 The scaling seems ok, but the performance is far from what I expected. In terms CPU-to-CPU performance, the Bluegene is 8 times slower than other clusters. For comparison, I also did the same simulation using 64 processors in a SGI cluster, and I got 2.8 hour/ns, which is roughly equivalent to using 512 cores in BlueGene/Q. I am wondering if the above benchmark results are reasonable or not? Or Am I doing something wrong in compiling? Any comments/suggestions are appreciated, thank you very much! Have a nice day! Jianguo -- 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] Can we connect two boxes together for the simulation?
editconf is a nice tool to create vacuum in your box. You can then insert one of your box into another box using cat box1.gro box2.gro, just remove the very last line in box1.gro. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 2:46 PM, Bao Kai paeanb...@gmail.com wrote: Hi, all, I want to do NPT simulations with different compositions first. Then I want to connect the two boxes to continue the NPT simulation. I mean, after simulations, we get two boxes with different compositions. Can we do that with gromacs? or how can we do that? Thanks. Best, Kai -- 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] Can we connect two boxes together for the simulation?
Hi, I guess the renumbering of the atoms and molecules will be a problem, especially when the two boxes contain the same type of the molecules. How can we handle that? Thanks. Best, Kai editconf is a nice tool to create vacuum in your box. You can then insert one of your box into another box using cat box1.gro box2.gro, just remove the very last line in box1.gro. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 2:46 PM, Bao Kai paeanball at gmail.com http://lists.gromacs.org/mailman/listinfo/gmx-users wrote: * Hi, all, I want to do NPT simulations with different compositions first. Then I want** to connect the two boxes to continue the NPT simulation. I mean, after simulations, we get two boxes with different compositions. Can we do that with gromacs? or how can we do that? Thanks. Best,** Kai** --** gmx-users mailing listgmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users** http://lists.gromacs.org/mailman/listinfo/gmx-users** * Please search the archive at** http://www.gromacs.org/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-request at gromacs.org. http://lists.gromacs.org/mailman/listinfo/gmx-users** * 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] Performance of Gromacs-4.6.1 on BlueGene/Q
BG CPUs are generally much slower (clock whose) but scale better. You should try to run on 64 CPUs on the Blue gene too for faire comparison. The number of CPUs per nodes is also an important factor: the more CPUs per nodes the more communications needs to be done. I observed a significant slow down while going from 16 to 32 CPUs nodes (recent intel) but using the same number of CPUs. On Jun 4, 2013, at 4:02 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Dear All, Has anyone has Gromacs benchmark on Bluegene/Q? I recently installed gromacs-461 on BG/Q using the following command: cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \ -DGMX_BUILD_OWN_FFTW=ON \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_XML=OFF \ -DCMAKE_INSTALL_PREFIX=/scratch/home/biilijg/package/gromacs-461 make make install After that, I did a benchmark simulation using a box of pure water containing 140k atoms. The command I used for the above test is: srun --ntasks-per-node=32 --overcommit /scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c box_md1.gro -x box_md1.xtc -g md1.log job_md1 And I got the following performance: Num. cores hour/ns 128 9.860 256 4.984 512 2.706 10241.544 20480.978 40920.677 The scaling seems ok, but the performance is far from what I expected. In terms CPU-to-CPU performance, the Bluegene is 8 times slower than other clusters. For comparison, I also did the same simulation using 64 processors in a SGI cluster, and I got 2.8 hour/ns, which is roughly equivalent to using 512 cores in BlueGene/Q. I am wondering if the above benchmark results are reasonable or not? Or Am I doing something wrong in compiling? Any comments/suggestions are appreciated, thank you very much! Have a nice day! Jianguo -- 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] Performance of Gromacs-4.6.1 on BlueGene/Q
On Tue, Jun 4, 2013 at 4:20 PM, XAvier Periole x.peri...@rug.nl wrote: BG CPUs are generally much slower (clock whose) but scale better. You should try to run on 64 CPUs on the Blue gene too for faire comparison. The number of CPUs per nodes is also an important factor: the more CPUs per nodes the more communications needs to be done. I observed a significant slow down while going from 16 to 32 CPUs nodes (recent intel) but using the same number of CPUs. Indeed. Moreover, there is not (yet) any instruction-level parallelism in the GROMACS kernels used on BG/Q, unlike for the x86 family. So there is a theoretical factor of four that is simply not being exploited. (And no, the compiler is not good enough to do it automatically ;-)) Mark On Jun 4, 2013, at 4:02 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Dear All, Has anyone has Gromacs benchmark on Bluegene/Q? I recently installed gromacs-461 on BG/Q using the following command: cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \ -DGMX_BUILD_OWN_FFTW=ON \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_XML=OFF \ -DCMAKE_INSTALL_PREFIX=/scratch/home/biilijg/package/gromacs-461 make make install After that, I did a benchmark simulation using a box of pure water containing 140k atoms. The command I used for the above test is: srun --ntasks-per-node=32 --overcommit /scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c box_md1.gro -x box_md1.xtc -g md1.log job_md1 And I got the following performance: Num. cores hour/ns 128 9.860 256 4.984 512 2.706 10241.544 20480.978 40920.677 The scaling seems ok, but the performance is far from what I expected. In terms CPU-to-CPU performance, the Bluegene is 8 times slower than other clusters. For comparison, I also did the same simulation using 64 processors in a SGI cluster, and I got 2.8 hour/ns, which is roughly equivalent to using 512 cores in BlueGene/Q. I am wondering if the above benchmark results are reasonable or not? Or Am I doing something wrong in compiling? Any comments/suggestions are appreciated, thank you very much! Have a nice day! Jianguo -- 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 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] Performance of Gromacs-4.6.1 on BlueGene/Q
Thank you, Mark and Xavier. The thing is that the cluster manager set the minimum number of cores of each jobs in Bluegene/Q is 128, so I can not use 64 cores. But according to the performance, 512 cores in Bluegene roughly equivalent to 64 cores in another cluster. Since there are 16 cores in each computational cards, the total number of cores I used in Bluegene//Q is num_cards times 16. So in my test, I acutally run simulations using different number of cards, from 8 to 256. The following is the script I submitted to bluegene using 128 computational cards: #!/bin/sh #SBATCH --nodes=128 # set Use 128 Compute Cards ( 1x Compute Card = 16 cores, 128x16 = 2048 cores ) #SBATCH --job-name=128x16x2 # set Job name #SBATCH -output=first-job-sample # set Output file #SBATCH --partition=training srun --ntasks-per-node=32 --overcommit /scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c box_md1.gro -x box_md1.xtc -g md1.log job_md1 Since bluegene/q accepts up to 4 tasks each core, I used 32 mpi tasks for each card (2 task per core). I tried --ntasks-per-node=64, but the simulations get much slower. Is there a optimized number for --ntasks-per-node? Cheers Jianguo From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Jianguo Li ljg...@yahoo.com.sg Sent: Tuesday, 4 June 2013, 22:32 Subject: Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q On Tue, Jun 4, 2013 at 4:20 PM, XAvier Periole x.peri...@rug.nl wrote: BG CPUs are generally much slower (clock whose) but scale better. You should try to run on 64 CPUs on the Blue gene too for faire comparison. The number of CPUs per nodes is also an important factor: the more CPUs per nodes the more communications needs to be done. I observed a significant slow down while going from 16 to 32 CPUs nodes (recent intel) but using the same number of CPUs. Indeed. Moreover, there is not (yet) any instruction-level parallelism in the GROMACS kernels used on BG/Q, unlike for the x86 family. So there is a theoretical factor of four that is simply not being exploited. (And no, the compiler is not good enough to do it automatically ;-)) Mark On Jun 4, 2013, at 4:02 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Dear All, Has anyone has Gromacs benchmark on Bluegene/Q? I recently installed gromacs-461 on BG/Q using the following command: cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \ -DGMX_BUILD_OWN_FFTW=ON \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_XML=OFF \ -DCMAKE_INSTALL_PREFIX=/scratch/home/biilijg/package/gromacs-461 make make install After that, I did a benchmark simulation using a box of pure water containing 140k atoms. The command I used for the above test is: srun --ntasks-per-node=32 --overcommit /scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c box_md1.gro -x box_md1.xtc -g md1.log job_md1 And I got the following performance: Num. cores hour/ns 128 9.860 256 4.984 512 2.706 1024 1.544 2048 0.978 4092 0.677 The scaling seems ok, but the performance is far from what I expected. In terms CPU-to-CPU performance, the Bluegene is 8 times slower than other clusters. For comparison, I also did the same simulation using 64 processors in a SGI cluster, and I got 2.8 hour/ns, which is roughly equivalent to using 512 cores in BlueGene/Q. I am wondering if the above benchmark results are reasonable or not? Or Am I doing something wrong in compiling? Any comments/suggestions are appreciated, thank you very much! Have a nice day! Jianguo -- 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 -- 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] Can we connect two boxes together for the simulation?
On 6/4/13 10:12 AM, Bao Kai wrote: Hi, I guess the renumbering of the atoms and molecules will be a problem, especially when the two boxes contain the same type of the molecules. How can we handle that? genconf -renumber -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] About coulmb Vanderrwalls cutoff
Dear Justin Thank you for yoyr Previuos reply I am using Gromos96 53a6 so i am using the following parameters ns_type = grid nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 is this value is reasonable ? But when i run the grommp i got warnings as follows nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file CNTPEPnvt.mdp]: You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = Shift (possibly with DispCorr) NOTE 3 [file CNTPEPnvt.mdp]: You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = PME-Switch or Reaction-Field-zero if Chnge vdwtupe=shift with disspCorr = DispCorr = EnerPres I have got the error as follows WARNING 2 [file CNTPEPnvt.mdp]: The sum of the two largest charge group radii (0.498722) is larger than rlist (0.90) - rvdw (1.40) How to to Avoid this error? (Due to warning grompp_d terminated ) Thanks In Advance -- 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 coulmb Vanderrwalls cutoff
On 6/4/13 11:25 AM, vidhya sankar wrote: Dear Justin Thank you for yoyr Previuos reply I am using Gromos96 53a6 so i am using the following parameters ns_type = grid nstlist = 5 rlist = 0.9 rcoulomb= 0.9 rvdw= 1.4 is this value is reasonable ? Yes. But when i run the grommp i got warnings as follows nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file CNTPEPnvt.mdp]: You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = Shift (possibly with DispCorr) NOTE 3 [file CNTPEPnvt.mdp]: You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = PME-Switch or Reaction-Field-zero if Chnge vdwtupe=shift with disspCorr = DispCorr= EnerPres I have got the error as follows WARNING 2 [file CNTPEPnvt.mdp]: The sum of the two largest charge group radii (0.498722) is larger than rlist (0.90) - rvdw (1.40) How to to Avoid this error? (Due to warning grompp_d terminated ) The notes and warnings arise from settings that are still incorrect. Gromos96 force fields do not use shifted potentials for vdW interactions; they are simply truncated at rvdw using a plain cutoff. The plain cutoff for Coulombic interactions is also wrong. The original Gromos96 development was done with a reaction field term, but more recent work has shown PME to be superior. -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] Performance of Gromacs-4.6.1 on BlueGene/Q
On Tue, Jun 4, 2013 at 4:50 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Thank you, Mark and Xavier. The thing is that the cluster manager set the minimum number of cores of each jobs in Bluegene/Q is 128, so I can not use 64 cores. But according to the performance, 512 cores in Bluegene roughly equivalent to 64 cores in another cluster. Since there are 16 cores in each computational cards, the total number of cores I used in Bluegene//Q is num_cards times 16. So in my test, I acutally run simulations using different number of cards, from 8 to 256. The following is the script I submitted to bluegene using 128 computational cards: #!/bin/sh #SBATCH --nodes=128 # set Use 128 Compute Cards ( 1x Compute Card = 16 cores, 128x16 = 2048 cores ) #SBATCH --job-name=128x16x2 # set Job name #SBATCH -output=first-job-sample # set Output file #SBATCH --partition=training srun --ntasks-per-node=32 --overcommit /scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c box_md1.gro -x box_md1.xtc -g md1.log job_md1 Since bluegene/q accepts up to 4 tasks each core, I used 32 mpi tasks for each card (2 task per core). I tried --ntasks-per-node=64, but the simulations get much slower. Is there a optimized number for --ntasks-per-node? The threads per core thing will surely be useless for GROMACS. Even our unoptimized kernels will saturate the available flops. There simply is nothing to overlap, so you net lose from the extra overhead. You should aim at 16 threads per node, one for each A2 core. Each of those 16 need not be an MPI process, however. There's some general background info here http://www.gromacs.org/Documentation/Acceleration_and_parallelization. Relevant to BG/Q is that you will be using real MPI and should use OpenMP and the Verlet kernels (see http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multi-level_parallelization.3a_MPI.2fthread-MPI_.2b_OpenMP). Finding the right balance of OpenMP threads per MPI process is hardware- and problem-dependent, so you will need to experiment there. 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] Re: gmx 4.6 mpi installation through openmpi?
Compile and install your own FFTW per the install guide? At least that eliminates a variable. Mark On Tue, Jun 4, 2013 at 2:53 PM, escajarro juan-manuel.casti...@mv.uni-kl.de wrote: I received this answer: Mark Abraham Mon, 03 Jun 2013 08:02:56 -0700 That looks like there's a PGI compiler getting used at some point (perhaps the internal FFTW build is picking up the CC environment var? I forget how that gets its compiler!). If you do find * -name config.log then perhaps you can see in that file what the FFTW build thinks about its compiler. Mark I found the config.log file and checked that the compiler being used to compile the internal FFTW is the same version of gcc that is used to compile the rest of Gromacs. In fact, I set the environment variable CC to gcc. I also tried to clean and compile from scratch the FFTW, but no success. I also tried to specify with the environment variable CMAKE_LIBRARY_PATH where the FFTW library is (in my case in gromacs-4.6/src/contrib/fftw/gmxfftw-prefix/lib), but I obtained the same error. Any other idea? Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/gmx-4-6-mpi-installation-through-openmpi-tp5006975p5008782.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] pullx file content with pull_geometry = position
Dear gromacs user, I run a simulation where I restrain two groups in a specific position with respect to one another: one is part of a protein (index group name: pull_group) the other is just one ion (index pull_group name r_60022). I have the following parameters in my mdp file: * ; Pull code pull= umbrella pull_geometry = position ; pull_dim= Y Y Y pull_start = no pull_ngroups= 1 pull_group0 = pull_group pull_group1 = r_60022 pull_init1 = -.4110 1.0700 1.7760 pull_rate1 = 0.0 pull_vec1 = -0.264 0.315 0.912 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 100 ; every 0.2 ps pull_nstfout= 100 ; every 0.2 ps ** So the ion should be restrained around the position pull_init1 with respect to the center of mass of the protein. Here is a sample of the obtained pullx.xvg file: ** @title Pull COM @xaxis label Time (ps) @yaxis label Position (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend 0 X @ s1 legend 0 Y @ s2 legend 0 Z @ s3 legend 1 dX @ s4 legend 1 dY @ s5 legend 1 dZ 0. 3.43102 5.2156 11.5301 -0.531018 1.0244 2.13988 0.2000 3.43096 5.21543 11.53 -0.544007 1.02157 2.14952 0.4000 3.43094 5.2146 11.5304 -0.551138 1.00177 2.12238 0.6000 3.43074 5.21354 11.5312 -0.559285 1.01417 2.13649 (...) 20. 3.45331 5.22215 11.51 -0.646908 0.9390662.11768 (...) 40. 3.45141 5.21115 11.5685 -0.689742 0.9789082.14589 (...) * As far as I understood the manual and after searching the forum I though that the first column is the time, the next three columns the position of the pulled group (r_60022) at the time and the last three columns the distance in the x y z direction between the reference group (pull_group, bad name choice I know) and the pulled group (r_60022). If that was true it would suggest that the ion is pulled more than three A away from the center of the umbrella potential. After checking the trajectory visually and by calculating the distance between pull_group and r_60022 using g_dist on the trajectory we can see it is not the case. Here is a sample of the g_dist output: @title Distance @xaxis label Time (ps) @yaxis label Distance (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend |d| @ s1 legend d\sx\N @ s2 legend d\sy\N @ s3 legend d\sz\N 0.0002.1085827 -0.37829451.13508751.7362576 20.0002.0527425 -0.44645331.07192131.6927538 40.0002.1132109 -0.34997841.12395621.7549639 (...) *** Which oscillate correctly around the pull_init1 vector as defined in the mdp file. More importantly these results are different from the results in the pullx.xvg file (at least the results I expected to have). Can somebody clarify what is actually in the pullx.xvg file ? Best, Bastien Loubet -- View this message in context: http://gromacs.5086.x6.nabble.com/pullx-file-content-with-pull-geometry-position-tp5008797.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] ngmx not installed in gmx4.6.1
Dear gmx users, I had installed gromacs 4.6.1 using cmake. All the binaries are installed, but surprisingly I do not find ngmx executable. Can anyone guide me how do I install ngmx using cmake. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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] ngmx not installed in gmx4.6.1
On 2013-06-04 17:55, Chandan Choudhury wrote: Dear gmx users, I had installed gromacs 4.6.1 using cmake. All the binaries are installed, but surprisingly I do not find ngmx executable. Can anyone guide me how do I install ngmx using cmake. cmake -DGMX_X11=ON Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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
Yes, documentation and output is not optimal. Resources are limited, sorry. Some of these issues are discussed in http://bugzilla.gromacs.org/issues/1135. The good news is that it sounds like you are having a non-problem. The output tacitly assumes heterogeneity. If your performance results are linear over small numbers of nodes, then you're doing fine. Mark 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
[gmx-users] pdb2gmx
Hello all, I am converting a .pdb into .gro and .top and assigning ClayFF forcefield, that is not included in the gromacs. It's a strange FF as doesn't have ones between all of the atoms, just O-H but it has an angle between a metal and OH, therefore I wore out molecule.rtp (see below) that included the angles, BUT wen I convert to the .top I only get bonds, but not angles (see below). Is there something I am missing or does gromacs not assign angles if no bonds are assigned? Thank you! molecule.rtp [ B31 ] ;# ldh21 [ atoms ] ; atomname atomtype charge chargegroup ; charges were taken from paper by Kuang Wu and J R Schmidt; J Phys Chem C (2012) ; and edited to make it fir LDH31 model and produce +1 o1 ohs -1.113 0 h1 ho 0.464 0 o2 ohs -1.113 0 h2 ho 0.464 0 o3 ohs -1.113 0 h3 ho 0.464 0 o4 ohs -1.113 0 h4 ho 0.464 0 mg1 mgo 1.403 0 al1 ao1.983 0 o5 ohs -1.113 0 h5 ho 0.464 0 o6 ohs -1.113 0 h6 ho 0.464 0 o7 ohs -1.113 0 h7 ho 0.464 0 o8 ohs -1.113 0 h8 ho 0.464 0 mg2 mgo 1.403 0 mg3 mgo 1.403 0 [ bonds ] ; atom1 atom2 parametersindex o1 h1 ohs o2 h2 ohs o3 h3 ohs o4 h4 ohs o5 h5 ohs o6 h6 ohs o7 h7 ohs o8 h8 ohs [ angles ] ; aiajak gromos type mg1 o1 h1 moh mg1 o8 h8 moh mg1 o4 h4 moh mg1 o6 h6 moh mg1 o3 h3 moh mg1 o5 h5 moh al1 o3 h3 moh al1 o5 h5 moh al1 o2 h2 moh al1 o7 h7 moh al1 o4 h4 moh al1 o6 h6 moh mg2 o8 h8 moh mg2 o2 h2 moh mg2 o5 h5 moh mg2 o4 h4 moh mg2 o7 h7 moh mg2 o1 h1 moh mg3 o7 h7 moh mg3 o1 h1 moh mg3 o6 h6 moh mg3 o3 h3 moh mg3 o8 h8 moh mg3 o2 h2 moh ldh31.top ; Include forcefield parameters #include ./ClayFF.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Other 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 B31 rtp B31 q +1.0 1ohs 1B31 o1 1 -1.113 16 ; qtot -1.113 2 ho 1B31 h1 1 0.464 1.008 ; qtot -0.649 3ohs 1B31 o2 1 -1.113 16 ; qtot -1.762 4 ho 1B31 h2 1 0.464 1.008 ; qtot -1.298 5ohs 1B31 o3 1 -1.113 16 ; qtot -2.411 6 ho 1B31 h3 1 0.464 1.008 ; qtot -1.947 7ohs 1B31 o4 1 -1.113 16 ; qtot -3.06 8 ho 1B31 h4 1 0.464 1.008 ; qtot -2.596 9mgo 1B31mg1 1 1.403 24.31 ; qtot -1.193 10 ao 1B31al1 1 1.983 26.98 ; qtot 0.79 11ohs 1B31 o5 1 -1.113 16 ; qtot -0.323 12 ho 1B31 h5 1 0.464 1.008 ; qtot 0.141 13ohs 1B31 o6 1 -1.113 16 ; qtot -0.972 14 ho 1B31 h6 1 0.464 1.008 ; qtot -0.508 15ohs 1B31 o7 1 -1.113 16 ; qtot -1.621 16 ho 1B31 h7 1 0.464 1.008 ; qtot -1.157 17ohs 1B31 o8 1 -1.113 16 ; qtot -2.27 18 ho 1B31 h8 1 0.464 1.008 ; qtot -1.806 19mgo 1B31mg2 1 1.403 24.31 ; qtot -0.403 20mgo 1B31mg3 1 1.403 24.31 ; qtot 1 [ bonds ] ; aiaj functc0c1c2c3 1 2 1ohs 3 4 1ohs 5 6 1ohs 7 8 1ohs 1112 1ohs 1314 1ohs 1516 1ohs 1718 1ohs ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name God Rules Over Mankind, Animals, Cosmos and Such [ molecules ] ; Compound#mols Other 1-- 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] ngmx not installed in gmx4.6.1
This has been default behaviour for years. See pre-conditions here http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_3.5._Optional_build_components. David's email has one way to solve the problem. Mark On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I had installed gromacs 4.6.1 using cmake. All the binaries are installed, but surprisingly I do not find ngmx executable. Can anyone guide me how do I install ngmx using cmake. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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] High Initial generated Temp
Thanks Justin. Sorry for not uploading the full .mdp. Here it is, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system comm_mode = linear energygrps = system ; 7.3.8 Output Control nstxout = 5000 nstfout = 5000 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc_precision = 1000 xtc_grps= System ; 7.3.9 Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.2 rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb= 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; 7.3.11 VdW vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 DispCorr= Ener ; 7.3.14 Temperature Coupling tcoupl = nose-hoover tc_grps = system tau_t = 1.0 ref_t = 300 ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300 gen_seed= 93873959697 ; 7.3.18 Bonds constraints = h-bonds constraint_algorithm= LINCS continuation= yes lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 Note: Using CHARMM27 force field I didn't use the 'continuation' part here. In the heating run I didn't put any constraints but in the production MD, I do apply constraints to the covalent bonds involving hydrogens. I just want to test the ligand movement inside the protein cavity in different set of initial velocities to get the feelings of how ligand is interacting with certain residues. So, then should I use these different velocity generating seeds during the warm up step? Thanks, Tarak On Tue, Jun 4, 2013 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/4/13 8:07 AM, tarak karmakar wrote: Dear All, Although I have set gen_temp = 300, it is showing the initial temperature 445.7 K, generated at the very beginning of the run. gen_vel = yes ; velocity generation gen_temp= 300 gen_seed= 93873959697 Is it because of a bad geometry? In mailing list I came across this thread [ http://comments.gmane.org/**gmane.science.biology.gromacs.**user/41931http://comments.gmane.org/gmane.science.biology.gromacs.user/41931 ] Prior to this production run, I heated my system slowly from 0 K to 300 K within 300 ps time span. It would be very helpful if someone suggests me the way to deal with this problem? A full .mdp file is always more useful than a small snippet. I have seen this same behavior when the continuation parameter is incorrectly set - have you used continuation = yes in your .mdp file? If not, the constraints get messed up and your initial velocities can get all messed up. A larger point is this - why are you re-generating velocities after heating the system from 0 to 300 K? Why not simply preserve the ensemble at 300 K by using a .cpt file? -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] High Initial generated Temp
I'm extremely sorry for copying the other '.mdp' file here. This is the modified one I just created after seeing your reply. In the previous case I didn't use 'continuation'. On Tue, Jun 4, 2013 at 9:47 PM, tarak karmakar tarak20...@gmail.com wrote: Thanks Justin. Sorry for not uploading the full .mdp. Here it is, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system comm_mode = linear energygrps = system ; 7.3.8 Output Control nstxout = 5000 nstfout = 5000 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc_precision = 1000 xtc_grps= System ; 7.3.9 Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.2 rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb= 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; 7.3.11 VdW vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 DispCorr= Ener ; 7.3.14 Temperature Coupling tcoupl = nose-hoover tc_grps = system tau_t = 1.0 ref_t = 300 ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300 gen_seed= 93873959697 ; 7.3.18 Bonds constraints = h-bonds constraint_algorithm= LINCS continuation= yes lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 Note: Using CHARMM27 force field I didn't use the 'continuation' part here. In the heating run I didn't put any constraints but in the production MD, I do apply constraints to the covalent bonds involving hydrogens. I just want to test the ligand movement inside the protein cavity in different set of initial velocities to get the feelings of how ligand is interacting with certain residues. So, then should I use these different velocity generating seeds during the warm up step? Thanks, Tarak On Tue, Jun 4, 2013 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/4/13 8:07 AM, tarak karmakar wrote: Dear All, Although I have set gen_temp = 300, it is showing the initial temperature 445.7 K, generated at the very beginning of the run. gen_vel = yes ; velocity generation gen_temp= 300 gen_seed= 93873959697 Is it because of a bad geometry? In mailing list I came across this thread [ http://comments.gmane.org/**gmane.science.biology.gromacs.**user/41931http://comments.gmane.org/gmane.science.biology.gromacs.user/41931 ] Prior to this production run, I heated my system slowly from 0 K to 300 K within 300 ps time span. It would be very helpful if someone suggests me the way to deal with this problem? A full .mdp file is always more useful than a small snippet. I have seen this same behavior when the continuation parameter is incorrectly set - have you used continuation = yes in your .mdp file? If not, the constraints get messed up and your initial velocities can get all messed up. A larger point is this - why are you re-generating velocities after heating the system from 0 to 300 K? Why not simply preserve the ensemble at 300 K by using a .cpt file? -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
Re: [gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration
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
Re: [gmx-users] High Initial generated Temp
On 6/4/13 12:17 PM, tarak karmakar wrote: Thanks Justin. Sorry for not uploading the full .mdp. Here it is, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system comm_mode = linear energygrps = system ; 7.3.8 Output Control nstxout = 5000 nstfout = 5000 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc_precision = 1000 xtc_grps= System ; 7.3.9 Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.2 rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb= 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; 7.3.11 VdW vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 DispCorr= Ener ; 7.3.14 Temperature Coupling tcoupl = nose-hoover tc_grps = system tau_t = 1.0 ref_t = 300 ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300 gen_seed= 93873959697 ; 7.3.18 Bonds constraints = h-bonds constraint_algorithm= LINCS continuation= yes lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 Note: Using CHARMM27 force field I didn't use the 'continuation' part here. In the heating run I didn't put any constraints but in the production MD, I do apply constraints to the covalent bonds involving hydrogens. I just want The introduction of constraints explains the observed behavior. You ran an unconstrained simulation, then at step 0 of the constrained simulation, the constraints have to be satisfied, which may introduce sudden movement in atomic positions, hence large velocities and a high temperature. The rule of thumb I always use - if you're going to use constraints during production simulations, use constraints during equilibration. I have seen several instances where unconstrained equilibration causes constrained simulations to later fail. to test the ligand movement inside the protein cavity in different set of initial velocities to get the feelings of how ligand is interacting with certain residues. So, then should I use these different velocity generating seeds during the warm up step? That's an interesting question. If you're warming from 0 - 300 K, I don't know how grompp will generate velocities at 0 K, but regenerating velocities after warming seems to defeat the purpose of doing the warming at all, in my mind, since you're just going to re-randomize the entire system by doing so. -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] GPU problem
On 06/04/2013 11:22 AM, Chandan Choudhury wrote: Hi Albert, I think using -nt flag (-nt=16) with mdrun would solve your problem. Chandan thank you so much. it works well now. ALBERT -- 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] Can we connect two boxes together for the simulation?
Nohow. Numbers in GRO files serve exclusively decorative function. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 4:12 PM, Bao Kai paeanb...@gmail.com wrote: Hi, I guess the renumbering of the atoms and molecules will be a problem, especially when the two boxes contain the same type of the molecules. How can we handle that? Thanks. Best, Kai editconf is a nice tool to create vacuum in your box. You can then insert one of your box into another box using cat box1.gro box2.gro, just remove the very last line in box1.gro. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 2:46 PM, Bao Kai paeanball at gmail.com http://lists.gromacs.org/mailman/listinfo/gmx-users wrote: * Hi, all, I want to do NPT simulations with different compositions first. Then I want** to connect the two boxes to continue the NPT simulation. I mean, after simulations, we get two boxes with different compositions. Can we do that with gromacs? or how can we do that? Thanks. Best,** Kai** --** gmx-users mailing list gmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users** http://lists.gromacs.org/mailman/listinfo/gmx-users** * Please search the archive at** http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting!** * Please don't post (un)subscribe requests to the list. Use the** www interface or send it to gmx-users-request at gromacs.org. http://lists.gromacs.org/mailman/listinfo/gmx-users** * 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 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] High Initial generated Temp
Yeah! It is indeed a silly point to generate a velocity distribution at 0 K. ( Maxwell-Boltzmann will be in trouble) After the warm up, now let say my protein is in 300 K, can't I generate a velocity distribution at 300 k (using the keyword gen_vel = yes, gen_temp = 300 K gen_seed = 173529 ) during my production run? Thanks, Tarak On Tue, Jun 4, 2013 at 10:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/4/13 12:17 PM, tarak karmakar wrote: Thanks Justin. Sorry for not uploading the full .mdp. Here it is, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system comm_mode = linear energygrps = system ; 7.3.8 Output Control nstxout = 5000 nstfout = 5000 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc_precision = 1000 xtc_grps= System ; 7.3.9 Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.2 rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb= 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; 7.3.11 VdW vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 DispCorr= Ener ; 7.3.14 Temperature Coupling tcoupl = nose-hoover tc_grps = system tau_t = 1.0 ref_t = 300 ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300 gen_seed= 93873959697 ; 7.3.18 Bonds constraints = h-bonds constraint_algorithm= LINCS continuation= yes lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 Note: Using CHARMM27 force field I didn't use the 'continuation' part here. In the heating run I didn't put any constraints but in the production MD, I do apply constraints to the covalent bonds involving hydrogens. I just want The introduction of constraints explains the observed behavior. You ran an unconstrained simulation, then at step 0 of the constrained simulation, the constraints have to be satisfied, which may introduce sudden movement in atomic positions, hence large velocities and a high temperature. The rule of thumb I always use - if you're going to use constraints during production simulations, use constraints during equilibration. I have seen several instances where unconstrained equilibration causes constrained simulations to later fail. to test the ligand movement inside the protein cavity in different set of initial velocities to get the feelings of how ligand is interacting with certain residues. So, then should I use these different velocity generating seeds during the warm up step? That's an interesting question. If you're warming from 0 - 300 K, I don't know how grompp will generate velocities at 0 K, but regenerating velocities after warming seems to defeat the purpose of doing the warming at all, in my mind, since you're just going to re-randomize the entire system by doing so. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] problems with GROMACS 4.6.2
Hi GROMACS users, It's come to our attention that some changes we made in 4.6.2 to the way we detect low-level hardware attributes sometimes affects mdrun performance. Specifically: * using real MPI will likely lead to lower performance than 4.6.1, if GROMACS managing the setting of thread affinities would have been a good thing * on Mac OS, mdrun might hang completely If the simulation runs, then it's correct :-) We've identified fixes and will release 4.6.3 in the next few days. In the meantime, we suggest not bothering to install 4.6.2. Apologies, 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] GPU problem
-nt is mostly a backward compatibility option and sets the total number of threads (per rank). Instead, you should set both -ntmpi (or -np with MPI) and -ntomp. However, note that unless a single mdrun uses *all* cores/hardware threads on a node, it won't pin the threads to cores. Failing to pin threads will lead to considerable performance degradation; just tried and depending on how (un)lucky the thread placement and migration is, I get 1.5-2x performance degradation with running two mdrun-s on a single dual-socket node without pining threads. My advise is (yet again) that you should check the http://www.gromacs.org/Documentation/Acceleration_and_parallelization wiki page, in particular the section on how to run simulations. If things are not, clear please ask for clarification - input and constructive criticism should help us improve the wiki. We have been patiently pointing everyone to the wiki, so asking without reading up first is neither productive nor really fair. Cheers, -- Szilárd On Tue, Jun 4, 2013 at 11:22 AM, Chandan Choudhury iitd...@gmail.com wrote: Hi Albert, I think using -nt flag (-nt=16) with mdrun would solve your problem. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Jun 4, 2013 at 12:56 PM, Albert mailmd2...@gmail.com wrote: Dear: I've got four GPU in one workstation. I am trying to run two GPU job with command: mdrun -s md.tpr -gpu_id 01 mdrun -s md.tpr -gpu_id 23 there are 32 CPU in this workstation. I found that each job trying to use the whole CPU, and there are 64 sub job when these two GPU mdrun submitted. Moreover, one of the job stopped after short of running, probably because of the CPU issue. I am just wondering, how can we distribute CPU when we run two GPU job in a single workstation? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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 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] problems with GROMACS 4.6.2
Just a few minor details: - You can set the affinities yourself through the job scheduler which should give nearly identical results compared to the mdrun internal affinity if you simply assign cores to mdrun threads in a sequential order (or with an #physical cores stride if you want to use HyperThreading); - At low parallelization and without OpenMP (i.e. -ntomp 1) you may not notice much regression even though threads won't be pinned. -- Szilárd On Tue, Jun 4, 2013 at 7:05 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi GROMACS users, It's come to our attention that some changes we made in 4.6.2 to the way we detect low-level hardware attributes sometimes affects mdrun performance. Specifically: * using real MPI will likely lead to lower performance than 4.6.1, if GROMACS managing the setting of thread affinities would have been a good thing * on Mac OS, mdrun might hang completely If the simulation runs, then it's correct :-) We've identified fixes and will release 4.6.3 in the next few days. In the meantime, we suggest not bothering to install 4.6.2. Apologies, 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
[gmx-users] Re: oxidized lipid - Peroxidated lipid
Dear All, I need to use oxidized lipids in my system. Any suggestion for force field that I can use would be appreciated. Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/oxidized-lipid-Peroxidated-lipid-tp5008661p5008810.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] ngmx not installed in gmx4.6.1
I do not know about the newest versions, but in older ones ngmx was missed when you did not have the lesstif library installed. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I had installed gromacs 4.6.1 using cmake. All the binaries are installed, but surprisingly I do not find ngmx executable. Can anyone guide me how do I install ngmx using cmake. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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] GPU problem
Dear All or anyone, A stupid question. Is there an script anyone knows of to convert a 53a6ff from .top redirects to the gromacs/top directory to something like a ligand .itp? This is usefull at the moment. Example: [bond] 6 7 2 gb_5 to [bonds] ; ai aj fu c0, c1, ... 6 7 2 0.139 1080.0 0.139 1080.0 ; C CH for everything (a protein/DNA complex) inclusive of angles, dihedrials? Ive been playing with some of the gromacs user supplied files, but nothing yet. Stephan Watkins -- 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] Performance of Gromacs-4.6.1 on BlueGene/Q
On Tue, Jun 4, 2013 at 5:48 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Tue, Jun 4, 2013 at 4:50 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Thank you, Mark and Xavier. The thing is that the cluster manager set the minimum number of cores of each jobs in Bluegene/Q is 128, so I can not use 64 cores. But according to the performance, 512 cores in Bluegene roughly equivalent to 64 cores in another cluster. Since there are 16 cores in each computational cards, the total number of cores I used in Bluegene//Q is num_cards times 16. So in my test, I acutally run simulations using different number of cards, from 8 to 256. The following is the script I submitted to bluegene using 128 computational cards: #!/bin/sh #SBATCH --nodes=128 # set Use 128 Compute Cards ( 1x Compute Card = 16 cores, 128x16 = 2048 cores ) #SBATCH --job-name=128x16x2 # set Job name #SBATCH -output=first-job-sample # set Output file #SBATCH --partition=training srun --ntasks-per-node=32 --overcommit /scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c box_md1.gro -x box_md1.xtc -g md1.log job_md1 Since bluegene/q accepts up to 4 tasks each core, I used 32 mpi tasks for each card (2 task per core). I tried --ntasks-per-node=64, but the simulations get much slower. Is there a optimized number for --ntasks-per-node? The threads per core thing will surely be useless for GROMACS. Even our unoptimized kernels will saturate the available flops. There simply is nothing to overlap, so you net lose from the extra overhead. You should aim at 16 threads per node, one for each A2 core. Each of those 16 need not be an MPI process, however. There's some general background info here http://www.gromacs.org/Documentation/Acceleration_and_parallelization. Relevant to BG/Q is that you will be using real MPI and should use OpenMP and the Verlet kernels (see http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multi-level_parallelization.3a_MPI.2fthread-MPI_.2b_OpenMP). Finding the right balance of OpenMP threads per MPI process is hardware- and problem-dependent, so you will need to experiment there. Thought I'd clarify further. A BG/Q node has 16 A2 cores. Some mix of MPI and OpenMP threads across those will be right for GROMACS. Each core is capable of running up to four hardware threads. The processor in each core can only issue two instructions per cycle, one flop and one non-flop, but only to two different hardware threads. There is a theoretical speedup from using more than one hardware thread, since you get to take advantage of more instruction-issue opportunities. But doing so with more MPI processes will incur other overhead (e.g. from PME global communication, as well as pure-MPI overhead). Even if you can map the extra hardware threads to OpenMP threads, you will only be able to get some fraction of the speedup depending on available registers and bandwidth from cache (and you still pay some extra overhead for the OpenMP). How big these effects are depend whether you are running PME, and which of the kernels you are actually executing. So it might be worth investigating 2 hardware threads per core using OpenMP, but don't expect to want to write home about the results! :-) Cheers, 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] High Initial generated Temp
On 6/4/13 12:51 PM, tarak karmakar wrote: Yeah! It is indeed a silly point to generate a velocity distribution at 0 K. ( Maxwell-Boltzmann will be in trouble) After the warm up, now let say my protein is in 300 K, can't I generate a velocity distribution at 300 k (using the keyword gen_vel = yes, gen_temp = 300 K gen_seed = 173529 ) during my production run? You can generate velocities whenever you like, but you'll have to allow for some time to equilibrate, so what you're calling production isn't entirely production because it's no longer equilibrated in any real sense. The heating phase may help to optimize the initial geometry, but regenerating velocities may screw everything up if something becomes unstable. Assuming restraints are off during production, then you can screw up the geometry of your system if something gets an unpleasant kick from the new velocities. -Justin On Tue, Jun 4, 2013 at 10:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/4/13 12:17 PM, tarak karmakar wrote: Thanks Justin. Sorry for not uploading the full .mdp. Here it is, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system comm_mode = linear energygrps = system ; 7.3.8 Output Control nstxout = 5000 nstfout = 5000 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc_precision = 1000 xtc_grps= System ; 7.3.9 Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.2 rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb= 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; 7.3.11 VdW vdwtype = switch rvdw= 1.2 rvdw-switch = 1.0 DispCorr= Ener ; 7.3.14 Temperature Coupling tcoupl = nose-hoover tc_grps = system tau_t = 1.0 ref_t = 300 ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300 gen_seed= 93873959697 ; 7.3.18 Bonds constraints = h-bonds constraint_algorithm= LINCS continuation= yes lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 Note: Using CHARMM27 force field I didn't use the 'continuation' part here. In the heating run I didn't put any constraints but in the production MD, I do apply constraints to the covalent bonds involving hydrogens. I just want The introduction of constraints explains the observed behavior. You ran an unconstrained simulation, then at step 0 of the constrained simulation, the constraints have to be satisfied, which may introduce sudden movement in atomic positions, hence large velocities and a high temperature. The rule of thumb I always use - if you're going to use constraints during production simulations, use constraints during equilibration. I have seen several instances where unconstrained equilibration causes constrained simulations to later fail. to test the ligand movement inside the protein cavity in different set of initial velocities to get the feelings of how ligand is interacting with certain residues. So, then should I use these different velocity generating seeds during the warm up step? That's an interesting question. If you're warming from 0 - 300 K, I don't know how grompp will generate velocities at 0 K, but regenerating velocities after warming seems to defeat the purpose of doing the warming at all, in my mind, since you're just going to re-randomize the entire system by doing so. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists --
Re: [gmx-users] Re: oxidized lipid - Peroxidated lipid
On 6/4/13 3:10 PM, dariush wrote: Dear All, I need to use oxidized lipids in my system. Any suggestion for force field that I can use would be appreciated. Googling turns up useful stuff like http://www.sciencedirect.com/science/article/pii/S0006349507716752. -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] GPU problem
On 6/4/13 3:52 PM, lloyd riggs wrote: Dear All or anyone, A stupid question. Is there an script anyone knows of to convert a 53a6ff from .top redirects to the gromacs/top directory to something like a ligand .itp? This is usefull at the moment. Example: [bond] 6 7 2gb_5 to [bonds] ; ai aj fuc0, c1, ... 6 7 20.139 1080.00.139 1080.0 ; C CH for everything (a protein/DNA complex) inclusive of angles, dihedrials? Ive been playing with some of the gromacs user supplied files, but nothing yet. Sounds like something grompp -pp should take care of. -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
Aw: Re: [gmx-users] GPU problem
Thanks, thats exact what I was looking for. Stephan Gesendet:Dienstag, 04. Juni 2013 um 22:28 Uhr Von:Justin Lemkul jalem...@vt.edu An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: [gmx-users] GPU problem On 6/4/13 3:52 PM, lloyd riggs wrote: Dear All or anyone, A stupid question. Is there an script anyone knows of to convert a 53a6ff from .top redirects to the gromacs/top directory to something like a ligand .itp? This is usefull at the moment. Example: [bond] 6 7 2 gb_5 to [bonds] ; ai aj fu c0, c1, ... 6 7 2 0.139 1080.0 0.139 1080.0 ; C CH for everything (a protein/DNA complex) inclusive of angles, dihedrials? Ive been playing with some of the gromacs user supplied files, but nothing yet. Sounds like something grompp -pp should take care of. -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 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant 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] pdb2gmx
On 6/4/13 12:05 PM, Valentina Erastova wrote: Hello all, I am converting a .pdb into .gro and .top and assigning ClayFF forcefield, that is not included in the gromacs. It's a strange FF as doesn't have ones between all of the atoms, just O-H but it has an angle between a metal and OH, therefore I wore out molecule.rtp (see below) that included the angles, BUT wen I convert to the .top I only get bonds, but not angles (see below). Is there something I am missing or does gromacs not assign angles if no bonds are assigned? That's probably correct, given that normally pdb2gmx will build angles based on bonds that are present. Most normal usage will never have angles without bonds, so for now, you will have to write the angles in the topology yourself. I will file a bug report with a (much simpler) test case so we don't lose track of this issue. Given that it affects so few simulations, it may be a while before it is resolved, but it may well be worth doing simply for flexibility reasons. -Justin Thank you! molecule.rtp [ B31 ] ;# ldh21 [ atoms ] ; atomname atomtype charge chargegroup ; charges were taken from paper by Kuang Wu and J R Schmidt; J Phys Chem C (2012) ; and edited to make it fir LDH31 model and produce +1 o1 ohs -1.113 0 h1 ho 0.464 0 o2 ohs -1.113 0 h2 ho 0.464 0 o3 ohs -1.113 0 h3 ho 0.464 0 o4 ohs -1.113 0 h4 ho 0.464 0 mg1 mgo 1.403 0 al1 ao1.983 0 o5 ohs -1.113 0 h5 ho 0.464 0 o6 ohs -1.113 0 h6 ho 0.464 0 o7 ohs -1.113 0 h7 ho 0.464 0 o8 ohs -1.113 0 h8 ho 0.464 0 mg2 mgo 1.403 0 mg3 mgo 1.403 0 [ bonds ] ; atom1 atom2 parametersindex o1 h1 ohs o2 h2 ohs o3 h3 ohs o4 h4 ohs o5 h5 ohs o6 h6 ohs o7 h7 ohs o8 h8 ohs [ angles ] ; aiajak gromos type mg1 o1 h1 moh mg1 o8 h8 moh mg1 o4 h4 moh mg1 o6 h6 moh mg1 o3 h3 moh mg1 o5 h5 moh al1 o3 h3 moh al1 o5 h5 moh al1 o2 h2 moh al1 o7 h7 moh al1 o4 h4 moh al1 o6 h6 moh mg2 o8 h8 moh mg2 o2 h2 moh mg2 o5 h5 moh mg2 o4 h4 moh mg2 o7 h7 moh mg2 o1 h1 moh mg3 o7 h7 moh mg3 o1 h1 moh mg3 o6 h6 moh mg3 o3 h3 moh mg3 o8 h8 moh mg3 o2 h2 moh ldh31.top ; Include forcefield parameters #include ./ClayFF.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Other 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 B31 rtp B31 q +1.0 1ohs 1B31 o1 1 -1.113 16 ; qtot -1.113 2 ho 1B31 h1 1 0.464 1.008 ; qtot -0.649 3ohs 1B31 o2 1 -1.113 16 ; qtot -1.762 4 ho 1B31 h2 1 0.464 1.008 ; qtot -1.298 5ohs 1B31 o3 1 -1.113 16 ; qtot -2.411 6 ho 1B31 h3 1 0.464 1.008 ; qtot -1.947 7ohs 1B31 o4 1 -1.113 16 ; qtot -3.06 8 ho 1B31 h4 1 0.464 1.008 ; qtot -2.596 9mgo 1B31mg1 1 1.403 24.31 ; qtot -1.193 10 ao 1B31al1 1 1.983 26.98 ; qtot 0.79 11ohs 1B31 o5 1 -1.113 16 ; qtot -0.323 12 ho 1B31 h5 1 0.464 1.008 ; qtot 0.141 13ohs 1B31 o6 1 -1.113 16 ; qtot -0.972 14 ho 1B31 h6 1 0.464 1.008 ; qtot -0.508 15ohs 1B31 o7 1 -1.113 16 ; qtot -1.621 16 ho 1B31 h7 1 0.464 1.008 ; qtot -1.157 17ohs 1B31 o8 1 -1.113 16 ; qtot -2.27 18 ho 1B31 h8 1 0.464 1.008 ; qtot -1.806 19mgo 1B31mg2 1 1.403 24.31 ; qtot -0.403 20mgo 1B31mg3 1 1.403 24.31 ; qtot 1 [ bonds ] ; aiaj functc0c1c2c3 1 2 1ohs 3 4 1ohs 5 6 1ohs 7 8 1ohs 1112 1ohs 1314 1ohs 1516 1ohs 1718 1ohs ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name God Rules Over Mankind, Animals, Cosmos and Such [ molecules ] ; Compound#mols Other 1-- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] About coulmb Vanderrwalls cutoff
Dear Justin Thank you for your Previous reply. As yo mailed me The Defaut Value for vandewalls and Electrostatics in GROMOS96 53A6 is PME option s_type = grid nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 But in you Umbrella sampling you are using GROMOS96 53A6 FF there you quoted different Parameters in your em.mdp file nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.4 ; Short-range electrostatic cut-off rvdw= 1.4 ; Short-range Van der Waals cut-off pbc = xyz can i Take 1.4 instead of 0.9 value oterwise is there is Any spcification according to system and BOx size Thanks Inadvance -- 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 coulmb Vanderrwalls cutoff
On 6/4/13 9:48 PM, vidhya sankar wrote: Dear Justin Thank you for your Previous reply. As yo mailed me The Defaut Value for vandewalls and Electrostatics in GROMOS96 53A6 is PME option s_type = grid nstlist = 5 rlist = 0.9 rcoulomb= 0.9 rvdw= 1.4 But in you Umbrella sampling you are usingGROMOS96 53A6 FF there you quoted different Parameters in your em.mdp file nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.4 ; Short-range electrostatic cut-off rvdw= 1.4 ; Short-range Van der Waals cut-off pbc = xyz can i Take 1.4 instead of 0.9 value The value of rcoulomb is a bit more flexible when using PME, but unless you have a basis for changing it (and having demonstrated that the change is harmless), you shouldn't deviate from the parameters given for the force field. oterwise is there is Any spcification according to system and BOx size The contents of the system and size of the box do not dictate the parameters that are set; the force field does. -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] About coulmb Vanderrwalls cutoff
Dear Justin thank you for your previous reply How can i check using th value 1.4 is harmless to My system Through g_energy ouput (potential.xvg) can i check (graphically) Thnaks In Advance -- 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] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field
Problem solved. Just as well I held off reporting the issue in full until I had explored everything, I would ended have look a bit stupid ;-) But asking the initial question helped direct my thinking to the reason. The issue was the difference in van der Waals cut off between the PME/Cut-off and Reaction Field methods that I was using, 0.9/0.9/0.9 vs 0.8/1.4/1.4 The difference was hidden in the results until you turned off Dispersion Correction, which was what was confusing me and final led to realizing what is going on. My forehead hurt from slapping it after coming to the realization ... It should also be noted (and obvious now that I actually look into it) that using dispersion correction results in both the latent heat of vapourisation and density of the alkanes being over estimated (for both Cut-off and Reaction Field, and by the same amount). Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Thursday, 30 May 2013 9:32 PM To: Vitaly Chaban; Discussion list for GROMACS users Subject: Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field Things should be identical - any quantity computed from a zero charge has to be zero :-). Mark On Thu, May 30, 2013 at 1:26 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Hmmm... And what does the observed difference look like, numerically? On Thu, May 30, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.com wrote: No charges = no problem. You can trivially test this yourself with mdrun -rerun ;-) Manual 4.1.4 talks about what RF is doing. Mark On Thu, May 30, 2013 at 6:38 AM, Dallas Warren dallas.war...@monash.edu wrote: In a system that has no charges, should we observe a difference between simulations using PME/Cut-offs or Reaction Field? From my understanding there should not be, since there are no charges which treatment you use shouldn't' make a difference. However, it does and I am trying to work out why. Any suggestions on the reason? What is it that Reaction Field is doing, does it influence anything other than long range charge interactions? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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 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 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
[gmx-users] restraints on water oxygen atoms
Dear gmx users, I have a POPC/peptide/water/ions system. I ran NVT and then NPT on my system. I'd prefer to run the equilibrium steps with position restraints on water oxygen atoms, because the water molecules penetrate the lipid bilayer when running the equilibrium and I don't want it to happen. I tried the NVT with position restraints on water by adding -DPOSRES_WATER to nvt.mdp file and editing the top file by changing the fc to 10. #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 10 10 10 #endif This edition turned into a better result. Now I tried to put such a restraint on npt but the gromacs does not allow it by turning a fatal error: A charge group moved too far between two domain decomposition steps. npt.mdp file: ;NPT equlibration Dimer-POPC-Water - CHARMM36 define = -DPOSRES_LIPID -DPOSRES -DPOSRES_WATER ; P headgroups of POPC and Protein is position restrained (uses the posres.itp file information) integrator = md ; leap-frog integrator nsteps =100 ; 1 * 100 = 1000 ps dt = 0.001 ; 1 fs ; Output control nstxout = 2000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 1000 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_Ces_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K pcoupl = Berendsen ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 310 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = Protein_POPC Water_Ces_CL refcoord_scaling = com I am wondering how it is possible to prevent penetrating the water molecules through equilibrium? And how I can put the restraint in npt as well as nvt? Would you please help me in this issue please? Sincerely, Shima -- 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] ngmx not installed in gmx4.6.1
Thanks David. It worked. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Jun 5, 2013 at 1:02 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: I do not know about the newest versions, but in older ones ngmx was missed when you did not have the lesstif library installed. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I had installed gromacs 4.6.1 using cmake. All the binaries are installed, but surprisingly I do not find ngmx executable. Can anyone guide me how do I install ngmx using cmake. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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 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