[gmx-users] Different energies of GPU and CPU-only runs with Gromacs 5.x
Dear all, if I compare GPU-accelerated and CPU-only runs, I get significantly different results/energies with Gromacs 5.x. In contrast, with Gromacs 4.x everything is fine, i.e. no difference between CPU-only runs and with GPU. In short, with Gromacs 5.x using GPUs, I have lower total energy, higher short-range LJ, higher short-range Coulomb and lower reciprocal Coulomb values. This also leads to altered density and box dimensions, etc The simulations were run on a single node with either 2x GeForce GTX 780 Ti or with 1x GTX 770. Compilers tested: gcc 4.8 and icc 14 Cuda Versions: 6.0 or 6.5 ForceField: Amber99sb-ildn The topol.tpr was identical for each simulation. Verlet cut-off scheme was used. The mdp file can be accessed here: https://www.dropbox.com/s/kjkglu2p8p11ajn/parameter.mdp?dl=0 Regression tests of the various compilations were always passed. Does someone has the some problems or has a clue what might cause the problems I have with Gromacs5.x when using GPUs ? Many thanks! Best, Jan-Philipp Machtens Postdoctoral Research Fellow Institute of Complex Systems - Cellular Biophysics (ICS-4) Forschungszentrum Jülich, Germany Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Different energies of GPU and CPU-only runs with Gromacs 5.x
On Mon, Sep 22, 2014 at 9:44 AM, Machtens, Jan-Philipp j.macht...@fz-juelich.de wrote: Dear all, if I compare GPU-accelerated and CPU-only runs, I get significantly different results/energies with Gromacs 5.x. In contrast, with Gromacs 4.x everything is fine, i.e. no difference between CPU-only runs and with GPU. In short, with Gromacs 5.x using GPUs, I have lower total energy, higher short-range LJ, higher short-range Coulomb and lower reciprocal Coulomb values. This is a normal consequence of different PME load balancing between CPU and GPU. You can use the UNIX diff tool to observe that mdrun is making different decisions. This also leads to altered density and box dimensions, etc MD trajectories are generally not reproducible even if the PME load is balanced the same way. Do replicates show the same kind of variation? Mark The simulations were run on a single node with either 2x GeForce GTX 780 Ti or with 1x GTX 770. Compilers tested: gcc 4.8 and icc 14 Cuda Versions: 6.0 or 6.5 ForceField: Amber99sb-ildn The topol.tpr was identical for each simulation. Verlet cut-off scheme was used. The mdp file can be accessed here: https://www.dropbox.com/s/kjkglu2p8p11ajn/parameter.mdp?dl=0 Regression tests of the various compilations were always passed. Does someone has the some problems or has a clue what might cause the problems I have with Gromacs5.x when using GPUs ? Many thanks! Best, Jan-Philipp Machtens Postdoctoral Research Fellow Institute of Complex Systems - Cellular Biophysics (ICS-4) Forschungszentrum Jülich, Germany Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Different energies of GPU and CPU-only runs with Gromacs 5.x
Thanks for the reply! However, the differences between GPU runs and CPU-only runs for Gromacs 5.x that I observe are statistically significant (10-100 ns for each test sim) (and reproducible). In contrast, with Gromacs 4.6.x I do not have significant differences that I can apparently attribute to the use of GPUs. Is there any other reason for the deviation with GPU and GROMAC 5.x ? Best, JP From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: Monday, September 22, 2014 10:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Different energies of GPU and CPU-only runs with Gromacs 5.x On Mon, Sep 22, 2014 at 9:44 AM, Machtens, Jan-Philipp j.macht...@fz-juelich.de wrote: Dear all, if I compare GPU-accelerated and CPU-only runs, I get significantly different results/energies with Gromacs 5.x. In contrast, with Gromacs 4.x everything is fine, i.e. no difference between CPU-only runs and with GPU. In short, with Gromacs 5.x using GPUs, I have lower total energy, higher short-range LJ, higher short-range Coulomb and lower reciprocal Coulomb values. This is a normal consequence of different PME load balancing between CPU and GPU. You can use the UNIX diff tool to observe that mdrun is making different decisions. This also leads to altered density and box dimensions, etc MD trajectories are generally not reproducible even if the PME load is balanced the same way. Do replicates show the same kind of variation? Mark The simulations were run on a single node with either 2x GeForce GTX 780 Ti or with 1x GTX 770. Compilers tested: gcc 4.8 and icc 14 Cuda Versions: 6.0 or 6.5 ForceField: Amber99sb-ildn The topol.tpr was identical for each simulation. Verlet cut-off scheme was used. The mdp file can be accessed here: https://www.dropbox.com/s/kjkglu2p8p11ajn/parameter.mdp?dl=0 Regression tests of the various compilations were always passed. Does someone has the some problems or has a clue what might cause the problems I have with Gromacs5.x when using GPUs ? Many thanks! Best, Jan-Philipp Machtens Postdoctoral Research Fellow Institute of Complex Systems - Cellular Biophysics (ICS-4) Forschungszentrum Jülich, Germany Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Different energies of GPU and CPU-only runs with Gromacs 5.x
On Mon, Sep 22, 2014 at 11:02 AM, Machtens, Jan-Philipp j.macht...@fz-juelich.de wrote: Thanks for the reply! However, the differences between GPU runs and CPU-only runs for Gromacs 5.x that I observe are statistically significant (10-100 ns for each test sim) (and reproducible). In contrast, with Gromacs 4.6.x I do not have significant differences that I can apparently attribute to the use of GPUs. OK. I would expect to observe a *total* energy that was constant across 4.6 and 5 and CPU-only vs with-GPUs. Please open an issue at http://redmine.gromacs.org/ and describe as much detail as you can. A tarball with .tpr, grompp-input, and whole .log files would let us analyze and reproduce your observations and work out what is going on. Thanks! Is there any other reason for the deviation with GPU and GROMAC 5.x ? Not by design :-) All the relevant changes that I can think of either removed code paths for old hardware, or tweaked performance (in various kinds of ways). There were a bunch of fixes introduced into 4.6.6 and 5.0 that could be relevant, but we need the gory details to know. Mark Best, JP From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: Monday, September 22, 2014 10:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Different energies of GPU and CPU-only runs with Gromacs 5.x On Mon, Sep 22, 2014 at 9:44 AM, Machtens, Jan-Philipp j.macht...@fz-juelich.de wrote: Dear all, if I compare GPU-accelerated and CPU-only runs, I get significantly different results/energies with Gromacs 5.x. In contrast, with Gromacs 4.x everything is fine, i.e. no difference between CPU-only runs and with GPU. In short, with Gromacs 5.x using GPUs, I have lower total energy, higher short-range LJ, higher short-range Coulomb and lower reciprocal Coulomb values. This is a normal consequence of different PME load balancing between CPU and GPU. You can use the UNIX diff tool to observe that mdrun is making different decisions. This also leads to altered density and box dimensions, etc MD trajectories are generally not reproducible even if the PME load is balanced the same way. Do replicates show the same kind of variation? Mark The simulations were run on a single node with either 2x GeForce GTX 780 Ti or with 1x GTX 770. Compilers tested: gcc 4.8 and icc 14 Cuda Versions: 6.0 or 6.5 ForceField: Amber99sb-ildn The topol.tpr was identical for each simulation. Verlet cut-off scheme was used. The mdp file can be accessed here: https://www.dropbox.com/s/kjkglu2p8p11ajn/parameter.mdp?dl=0 Regression tests of the various compilations were always passed. Does someone has the some problems or has a clue what might cause the problems I have with Gromacs5.x when using GPUs ? Many thanks! Best, Jan-Philipp Machtens Postdoctoral Research Fellow Institute of Complex Systems - Cellular Biophysics (ICS-4) Forschungszentrum Jülich, Germany Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
[gmx-users] profiler
Does anyone know that how to use NVIDIA Visual Profiler to profile gromacs-5.0? xiexiao...@sjtu.edu.cn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to rolled up a polymer chain
My goal, for now, is to model a polimer (nylon-6) chain, and to find the equilibrium position of the chain considering the capacity to be rolled up itself. I had create a pdb file using Avogadro software, but when i go to gromacs to input the data using the function pdb2gmx And indipendently of the force field that i choose i get :that Residue LIG not found. How to solve this? thanks MARCELLO CAMMARATA Ing., Ph.D., 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] I: How to rolled up a polymer chain
Hi, i had checked all the archives, i have read about 100posts in the last 2 month. Nobody have problem similar to mine. Problem for me are Two. 1- instead i am a doctor, i am not able to find the right advice at your site. 2- In your site there is no space for begginer user. The main pages where i checked are: Residue Chain Polyethylene (PE) simulations in Gromacs - please! .rtp File Force Fields Adding a Residue to a Force Field Modifying a force field But i don't have find any suggestion for my problem. Is there an other blog, that i can't see. i have several of problem with Gromacs, - in Cygwin it doen't work, i got a bash comand - the topology need a lig parameters. one more time, below there is my post. I wpould like if you can help me to solve this question, instead i can try to use an othere MD software. MARCELLO CAMMARATA Ing., Ph.D., 3208790796 Il Lunedì 22 Settembre 2014 14:20, marcello cammarata mstaxmarce...@yahoo.it ha scritto: My goal, for now, is to model a polimer (nylon-6) chain, and to find the equilibrium position of the chain considering the capacity to be rolled up itself. I had create a pdb file using Avogadro software, but when i go to gromacs to input the data using the function pdb2gmx And indipendently of the force field that i choose i get :that Residue LIG not found. How to solve this? thanks MARCELLO CAMMARATA Ing., Ph.D., 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] I: How to rolled up a polymer chain
Add the parameters for LIG residue in force filed. In that give information about the LIG in rtp file nonbonded file bonded file I think then it will work. On Mon, Sep 22, 2014 at 5:46 AM, marcello cammarata mstaxmarce...@yahoo.it wrote: Hi, i had checked all the archives, i have read about 100posts in the last 2 month. Nobody have problem similar to mine. Problem for me are Two. 1- instead i am a doctor, i am not able to find the right advice at your site. 2- In your site there is no space for begginer user. The main pages where i checked are: Residue Chain Polyethylene (PE) simulations in Gromacs - please! .rtp File Force Fields Adding a Residue to a Force Field Modifying a force field But i don't have find any suggestion for my problem. Is there an other blog, that i can't see. i have several of problem with Gromacs, - in Cygwin it doen't work, i got a bash comand - the topology need a lig parameters. one more time, below there is my post. I wpould like if you can help me to solve this question, instead i can try to use an othere MD software. MARCELLO CAMMARATA Ing., Ph.D., 3208790796 Il Lunedì 22 Settembre 2014 14:20, marcello cammarata mstaxmarce...@yahoo.it ha scritto: My goal, for now, is to model a polimer (nylon-6) chain, and to find the equilibrium position of the chain considering the capacity to be rolled up itself. I had create a pdb file using Avogadro software, but when i go to gromacs to input the data using the function pdb2gmx And indipendently of the force field that i choose i get :that Residue LIG not found. How to solve this? thanks MARCELLO CAMMARATA Ing., Ph.D., 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- regards M.SathishKumar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding error in grompp while running the tutorial of KALP15 in DPPC
On 9/22/14 4:48 AM, Anurag Dobhal wrote: I am getting an error while running the commmand gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr Fatal error: Unknown atomtype OW please help !!! You deleted a necessary atom type. Follow the instructions carefully and re-create the force field. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] I: How to rolled up a polymer chain
On 9/22/14 8:46 AM, marcello cammarata wrote: Hi, i had checked all the archives, i have read about 100posts in the last 2 month. Nobody have problem similar to mine. Problem for me are Two. 1- instead i am a doctor, i am not able to find the right advice at your site. 2- In your site there is no space for begginer user. The main pages where i checked are: Residue Chain Polyethylene (PE) simulations in Gromacs - please! .rtp File Force Fields Adding a Residue to a Force Field Modifying a force field All the information you need are in the above pages. You may want to do some simple tutorial material on known species before diving into something that requires detailed knowledge of Gromacs file formats and topology organization. There is basically a how-to at http://www.gromacs.org/Documentation/How-tos/Polymers But i don't have find any suggestion for my problem. Is there an other blog, that i can't see. i have several of problem with Gromacs, - in Cygwin it doen't work, i got a bash comand - the topology need a lig parameters. one more time, below there is my post. I wpould like if you can help me to solve this question, instead i can try to use an othere MD software. You'll encounter the same problem in just about every software you use. If you're using a molecule that is unknown to the force field, you're going to have to modify force field and/or topology files in some way. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding gromacs installation
On 9/22/14 3:00 AM, Anurag Dobhal wrote: I have followed the following steps for installaing gromacs 5.0.1 tar xfz gromacs-5.0.1.tar.gz cd gromacs-5.0.1 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC please tell me weather these steps are enough to install gromacs or do i need to do some thing more. In a simple sense, if it worked, then sure, that's all you need to do. Whether or not that's the best way to install Gromacs on your system is another matter, but that's why we provide http://www.gromacs.org/Documentation/Installation_Instructions -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Hello Regarding Lincs error
On 9/22/14 1:23 AM, RINU KHATTRI wrote: hello justin yes i did minimization and equilibrium i have one confusion when i am going for extension of simulation by tpbconv -s md_0_1.tpr -extend 9000 -o nextr.tpr for mdrun i have to use which checkpoint file md_0_1.cpt after 1 ns or state.cpt i am always confused with it i am usin 4.5.5 so append is default still the outputfile of 1st run is not appended just backoff traj,trr to #traj.trr.1# mdrun -s nextr.tpr -cpi state.cpt or mdrun -s nextr -cpi md_0_1.cpt kindly help I have no idea. How did you name your files? Do state.cpt and md_0_1.cpt co-exist? What is in them? If you ran a 1-ns simulation with mdrun -deffnm md_0_1, then you extend using md_0_1.cpt. This is why I always name my files descriptively or organize different parts of a simulation (equilibration, production intervals, etc) in different directories. -Justin On Thu, Sep 18, 2014 at 5:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/18/14 6:38 AM, RINU KHATTRI wrote: hello i am also facing the same problem i worked on the protein complex (popc ) but once again i am using same procedure its gives error even i changed .mdp file parameters Changed to what? From what? after running it gives 61% mdrun grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr mdrun -nt 4 -deffnm npt Did previous minimization and/or equilibration runs succeed? -Justin kindly help On Thu, Sep 18, 2014 at 2:23 PM, Ujwala Patil ujwalanpa...@gmail.com wrote: Hello I am doing simulation of dioxane+ water system during energy minimization i got error Too many LINCS warnings (1337) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem my em.mdp file is integrator = steep ; emtol = 500.0 emstep = 0.01 nsteps = 500 nstlist = 1.4 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.4 constraints = none pbc = xyz i have seen some similar type of error but not able to fix please help me to solve the problem -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] I: How to rolled up a polymer chain
Hi. I noticed mis-spellings in manual of another MD software that persisted throughout its versions. Googling for polyethylene simulation gave this article as first result: http://arxiv.org/pdf/1401.4295v1.pdf, which use lammps. I'm not sure about the availability, accuracy, and computation cost of the force field that they talk about. Personally, I guess simulation is like a film or drama. Using the right setup and looking from the correct angle (like from the front of the stage) give reasonable results. Using the wrong setup, or looking from the wrong direction (like from the side-way of the stage) can give wrong result. On Mon, Sep 22, 2014 at 8:50 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/22/14 8:46 AM, marcello cammarata wrote: Hi, i had checked all the archives, i have read about 100posts in the last 2 month. Nobody have problem similar to mine. Problem for me are Two. 1- instead i am a doctor, i am not able to find the right advice at your site. 2- In your site there is no space for begginer user. The main pages where i checked are: Residue Chain Polyethylene (PE) simulations in Gromacs - please! .rtp File Force Fields Adding a Residue to a Force Field Modifying a force field All the information you need are in the above pages. You may want to do some simple tutorial material on known species before diving into something that requires detailed knowledge of Gromacs file formats and topology organization. There is basically a how-to at http://www.gromacs.org/ Documentation/How-tos/Polymers But i don't have find any suggestion for my problem. Is there an other blog, that i can't see. i have several of problem with Gromacs, - in Cygwin it doen't work, i got a bash comand - the topology need a lig parameters. one more time, below there is my post. I wpould like if you can help me to solve this question, instead i can try to use an othere MD software. You'll encounter the same problem in just about every software you use. If you're using a molecule that is unknown to the force field, you're going to have to modify force field and/or topology files in some way. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gromacs error
hi guys i have a problems with gromacs command .how can i can solve this problems: i install gromacs and i dont know what can i do: gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top No command 'gmx' found, did you mean: Command 'gcx' from package 'gcx' (universe) Command 'ngmx' from package 'gromacs' (universe) Command 'gm' from package 'graphicsmagick' (universe) Command 'gmt' from package 'libgenome-perl' (universe) gmx: command not found and other problem : solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top solvate: command not found thank you for your help. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs error
On 9/22/14 10:14 AM, Yaser Hosseini wrote: hi guys i have a problems with gromacs command .how can i can solve this problems: i install gromacs and i dont know what can i do: gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top No command 'gmx' found, did you mean: Command 'gcx' from package 'gcx' (universe) Command 'ngmx' from package 'gromacs' (universe) Command 'gm' from package 'graphicsmagick' (universe) Command 'gmt' from package 'libgenome-perl' (universe) gmx: command not found You haven't configured your environment properly. http://www.gromacs.org/Documentation/Installation_Instructions#getting-access-to-gromacs-after-installation and other problem : solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top solvate: command not found That's not a valid command. gmx solvate is, if you follow the instructions above. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] profiler
The same way as you would use it with any other code. If you are not familiar with the tools, I suggest you read the documentation; there are tutorials available too e.g. http://devblogs.nvidia.com/parallelforall/cuda-pro-tip-nvprof-your-handy-universal-gpu-profiler/ and there should be recorded sessions online from the GTC conferences. -- Szilárd On Mon, Sep 22, 2014 at 1:12 PM, xiexiao...@sjtu.edu.cn xiexiao...@sjtu.edu.cn wrote: Does anyone know that how to use NVIDIA Visual Profiler to profile gromacs-5.0? xiexiao...@sjtu.edu.cn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the growth of the molecule
Thanks to everyone I have idea that I can stop simulation, change topology(move end of molecule, add new atoms) and start again. It should be repeated every 2 ps. But it can be very slowly. Does anybody know how to do it more correctly? 2014-09-18 20:03 GMT+07:00 Tamas Karpati tkarp...@gmail.com: Dear Alexander, As Vitaly has already suggested, it is possible to simulate growth. I'd, on the other hand, underline what Micholas has said. It may take some planning. Here are a few ideas how to do it. 1. If you are simulating cleaving/forming bonds, the topology would change which is difficult for normal MD runs. If, however, running just few steps (or probably a single step) MD job and analysing/regenerating the topology after each such step (by your specific scripts) you may be fine. It can take some coding. 2. You can still go on by replacing explicite bonds by Morse or LJ potentials (or using any tabled ones). Although such model can be poor in describing the underlying chemistry a good fitting of Morse/LJ/etc. can give you an acceptable rate for the polymerisation. This way bonds could be described by formally non-bonding interactions and the whole system is modelled as an interacting set of individual single atom ions. A complete replacement of all the bonds by non-bonding interaction potentials will give you a bond-less and angle-less etc. TOP file. It can be done in parts, too, in which case just some kinds of bonds (those that cleave or form) would be replaced. It may take lots of preparation but I think its viable. 3. Sorry, I know nothing about special force fields created for sims of reactions. Probably those would be your tools. HTH, toma On Thu, Sep 18, 2014 at 2:10 PM, Smith, Micholas D. smit...@ornl.gov wrote: I should clarify, If you are not concerned with the formation of covalent bonds, you can simulate growth, to some extent. Protein aggregation, for instance, can be studied with MD because of this; so if you are only interested in the early assembly, and not with electronic structure/covalent bonding, than you are ok. I had interpreted your question to be related to bonding, not just early assembly/aggregation. As far as adding units at a given time, I don't think gromacs can do that, as it would require your topology to change while the simulation was running (i.e. adding more molecules to your system while it is running). Now you could run multiple simulations of the polyethylene chain at different lengths with a single unit free in solution, and watch how the chain increases, but I don't think you could run a single simulation where you added monomer units on the fly. -Micholas From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Dr. Vitaly Chaban vvcha...@gmail.com Sent: Thursday, September 18, 2014 2:43 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] the growth of the molecule Why not? Your interaction potential is responsible for everything. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Mon, Sep 15, 2014 at 7:27 PM, Александр Селютин saga1...@gmail.com wrote: Can the gromacs simulate the growth of the molecule? For example, does it allow to add units to the polymer chain at certain times? More specifically, it is the increase the chain length of the polyethylene. Thanks! -- Regards, Alexander Selyutin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] can we do FEP MAPPER calculation in Gromacs?
Hello: I just found a pretty nice free energy calculation methods: FEP MAPPER. It can make a energy circle between different scalefold ligands which improved a lot for the free energy values. https://simtk.org/home/leadoptmap I am just wondering, is it possible to do it in Gromacs? Thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MD analysis
Dear all, I have carried out simulations of two homologous proteins (~38kDA) using Gromacs v4.5.3 using OPLS force field. The protein consists of three domains. Structural studies using cystallography reported earlier showed that the two proteins differ in the extent of orientations one domain can take with respect to other. However the reason for this difference is not clear from the structure as the size of the domain and region connecting them is almost the same in both. The only difference between the two are 32 residues spread over the sequence. Can anybody please suggest me as to how to go about with the MD analysis to find out the reason for this difference in the two structures ? Visualization of the structures extracted from the trajectory showed the domain to be flexible in two proteins but to different extents. Thanking You, regards Anu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the growth of the molecule
On 9/22/14 10:45 AM, Александр Селютин wrote: Thanks to everyone I have idea that I can stop simulation, change topology(move end of molecule, add new atoms) and start again. It should be repeated every 2 ps. But it can be very slowly. Does anybody know how to do it more correctly? I don't know that there is a good solution. What you've outlined also doesn't seem very reliable, because you're causing serious perturbations to the system every 2 ps, so the outcome of the previous simulation is basically lost because you have changed the coordinates and perturbed the solvent around the polymer. So you basically have a certain number of unequilibrated polymer systems of varying size. It doesn't help you to determine much of anything. MD is great for simulating nonbonded aggregation/assembly, but it is not trivial to do something involving covalent bonds in classical MD. -Justin 2014-09-18 20:03 GMT+07:00 Tamas Karpati tkarp...@gmail.com: Dear Alexander, As Vitaly has already suggested, it is possible to simulate growth. I'd, on the other hand, underline what Micholas has said. It may take some planning. Here are a few ideas how to do it. 1. If you are simulating cleaving/forming bonds, the topology would change which is difficult for normal MD runs. If, however, running just few steps (or probably a single step) MD job and analysing/regenerating the topology after each such step (by your specific scripts) you may be fine. It can take some coding. 2. You can still go on by replacing explicite bonds by Morse or LJ potentials (or using any tabled ones). Although such model can be poor in describing the underlying chemistry a good fitting of Morse/LJ/etc. can give you an acceptable rate for the polymerisation. This way bonds could be described by formally non-bonding interactions and the whole system is modelled as an interacting set of individual single atom ions. A complete replacement of all the bonds by non-bonding interaction potentials will give you a bond-less and angle-less etc. TOP file. It can be done in parts, too, in which case just some kinds of bonds (those that cleave or form) would be replaced. It may take lots of preparation but I think its viable. 3. Sorry, I know nothing about special force fields created for sims of reactions. Probably those would be your tools. HTH, toma On Thu, Sep 18, 2014 at 2:10 PM, Smith, Micholas D. smit...@ornl.gov wrote: I should clarify, If you are not concerned with the formation of covalent bonds, you can simulate growth, to some extent. Protein aggregation, for instance, can be studied with MD because of this; so if you are only interested in the early assembly, and not with electronic structure/covalent bonding, than you are ok. I had interpreted your question to be related to bonding, not just early assembly/aggregation. As far as adding units at a given time, I don't think gromacs can do that, as it would require your topology to change while the simulation was running (i.e. adding more molecules to your system while it is running). Now you could run multiple simulations of the polyethylene chain at different lengths with a single unit free in solution, and watch how the chain increases, but I don't think you could run a single simulation where you added monomer units on the fly. -Micholas From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Dr. Vitaly Chaban vvcha...@gmail.com Sent: Thursday, September 18, 2014 2:43 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] the growth of the molecule Why not? Your interaction potential is responsible for everything. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Mon, Sep 15, 2014 at 7:27 PM, Александр Селютин saga1...@gmail.com wrote: Can the gromacs simulate the growth of the molecule? For example, does it allow to add units to the polymer chain at certain times? More specifically, it is the increase the chain length of the polyethylene. Thanks! -- Regards, Alexander Selyutin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read
Re: [gmx-users] MD analysis
On 9/22/14 2:26 PM, Anu Chandran wrote: Dear all, I have carried out simulations of two homologous proteins (~38kDA) using Gromacs v4.5.3 using OPLS force field. The protein consists of three domains. Structural studies using cystallography reported earlier showed that the two proteins differ in the extent of orientations one domain can take with respect to other. However the reason for this difference is not clear from the structure as the size of the domain and region connecting them is almost the same in both. The only difference between the two are 32 residues spread over the sequence. Can anybody please suggest me as to how to go about with the MD analysis to find out the reason for this difference in the two structures ? Visualization of the structures extracted from the trajectory showed the domain to be flexible in two proteins but to different extents. Start by quantifying this. Unless you reproduce some experimental observable, looking for a mechanism behind it is useless without knowing if it is there. Also realize that a crystal environment is wildly different from a solution environment (and crystal packing effects can be very prominent); you generally won't see the same dynamics, so relating such flexibility back to the crystal structure may not even be possible. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the growth of the molecule
On Mon, Sep 22, 2014 at 7:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/22/14 10:45 AM, Александр Селютин wrote: Thanks to everyone I have idea that I can stop simulation, change topology(move end of molecule, add new atoms) and start again. It should be repeated every 2 ps. But it can be very slowly. Does anybody know how to do it more correctly? I don't know that there is a good solution. What you've outlined also doesn't seem very reliable, because you're causing serious perturbations to the system every 2 ps, so the outcome of the previous simulation is basically lost because you have changed the coordinates and perturbed the solvent around the polymer. So you basically have a certain number of unequilibrated polymer systems of varying size. It doesn't help you to determine much of anything. MD is great for simulating nonbonded aggregation/assembly, but it is not trivial to do something involving covalent bonds in classical MD. If you want to study dynamic of growth of materials via formation of chemical bonds (covalent, ionic and even metallic), perhaps empirical reactive FFs might be acceptable choices in terms of cost and accuracy BUT those are not implemented in GROMACS as far as I know. You need try them using LAMMPS, ADF, ReaxFF codes,. Rasoul 2014-09-18 20:03 GMT+07:00 Tamas Karpati tkarp...@gmail.com: Dear Alexander, As Vitaly has already suggested, it is possible to simulate growth. I'd, on the other hand, underline what Micholas has said. It may take some planning. Here are a few ideas how to do it. 1. If you are simulating cleaving/forming bonds, the topology would change which is difficult for normal MD runs. If, however, running just few steps (or probably a single step) MD job and analysing/regenerating the topology after each such step (by your specific scripts) you may be fine. It can take some coding. 2. You can still go on by replacing explicite bonds by Morse or LJ potentials (or using any tabled ones). Although such model can be poor in describing the underlying chemistry a good fitting of Morse/LJ/etc. can give you an acceptable rate for the polymerisation. This way bonds could be described by formally non-bonding interactions and the whole system is modelled as an interacting set of individual single atom ions. A complete replacement of all the bonds by non-bonding interaction potentials will give you a bond-less and angle-less etc. TOP file. It can be done in parts, too, in which case just some kinds of bonds (those that cleave or form) would be replaced. It may take lots of preparation but I think its viable. 3. Sorry, I know nothing about special force fields created for sims of reactions. Probably those would be your tools. HTH, toma On Thu, Sep 18, 2014 at 2:10 PM, Smith, Micholas D. smit...@ornl.gov wrote: I should clarify, If you are not concerned with the formation of covalent bonds, you can simulate growth, to some extent. Protein aggregation, for instance, can be studied with MD because of this; so if you are only interested in the early assembly, and not with electronic structure/covalent bonding, than you are ok. I had interpreted your question to be related to bonding, not just early assembly/aggregation. As far as adding units at a given time, I don't think gromacs can do that, as it would require your topology to change while the simulation was running (i.e. adding more molecules to your system while it is running). Now you could run multiple simulations of the polyethylene chain at different lengths with a single unit free in solution, and watch how the chain increases, but I don't think you could run a single simulation where you added monomer units on the fly. -Micholas From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Dr. Vitaly Chaban vvcha...@gmail.com Sent: Thursday, September 18, 2014 2:43 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] the growth of the molecule Why not? Your interaction potential is responsible for everything. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Mon, Sep 15, 2014 at 7:27 PM, Александр Селютин saga1...@gmail.com wrote: Can the gromacs simulate the growth of the molecule? For example, does it allow to add units to the polymer chain at certain times? More specifically, it is the increase the chain length of the polyethylene. Thanks! -- Regards, Alexander Selyutin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please
Re: [gmx-users] Some Scaling of 5.0 Results
Additionally to Mark's comments, let me ask/add a couple of things. What was your benchmarking procedure on core counts that represent less than a full socket? Besides the thread affinity issue mentioned by Mark, clock frequency scaling (boost) can also distort performance plots. You will observe artificially high performance on small core counts making the scaling inherently worse - unless this is explicitly turned off in the BIOS/firmware. This can be further enhanced by the low cache traffic when only partially using a multicore CPU. These are both artificial effects that you won't see in real-world runs - unless leaving a bunch of cores empty. There is no single right way to avoid these issues, there certainly are ways to present data in a less than useful manner - especially when it comes to scaling plots. A simple way of avoiding such issues and eliminating the potential for incorrect strong scaling plots is to start from at least a socket (or node). Otherwise, IMO the 8 threads data points on your plot make sense only if you show strong scaling to multiple sockets/nodes by using the same amount of threads per socket as you started with, leaving the rest of the cores free. What run configuration did you use for Verlet on single node? With the Verlet scheme no domain decomposition, that is multithreding-only (OpenMP) runs are typically more efficient than using domain-decomposition. This is typically true up to a full socket and quite often even across two Intel sockets. Did you tune the PME performance, i.e. the number of separate PME ranks? Did you use nstlist=40 for all Verlet data points? That may not be optimal across all node counts, especially on less than two nodes, but of course that's hard to tell without trying! Finally, looking at octanol Verlet plot, especially in comparison with the water plot, what's strange is that the scaling efficiency is much worse than with water and varies quite greatly between neighboring data points. This indicates that something was not entirely right with those runs. Cheers, -- Szilárd On Fri, Sep 19, 2014 at 1:35 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Sep 19, 2014 at 2:50 AM, Dallas Warren dallas.war...@monash.edu wrote: Some scaling results that might be of interest to some people. Machine = Barcoo @ VLSCI 2.7GHz Intel Sandybridge cores 256GB RAM 16 cores per node Mellanox FDR14 InfiniBand switch Systems = water and octanol only with GROMOS53a6 # Atoms = 10,000 to 1,000,000 Comparison Group versus Verlet neighbour searching Image/graphs see https://twitter.com/dr_dbw/status/512763354566254592 Basically group neighbour searching for this setup is faster and scales better than Verlet. Was expecting that to be the case with water, since it is mentioned somewhere that is the case. However for the pure octanol system was expecting it to be the other way around? Thanks for sharing. Since the best way to write code that scales well is to write code that runs slowly, we generally prefer to look at raw ns/day. Choosing between perfect scaling of implementation A at 10 ns/day and imperfect scaling of implementation B starting at 50 ns/day is a no-brainer, but only if you know the throughput. I'd also be very suspicious of your single-core result, based on your super-linear scaling. When using a number of cores smaller than a node, you need to take care to pin that thread (mdrun -pin on), and not having other processes also running on that core/node. If that result is noisy because it ran into different other stuff over time, then every scaling data point is affected. Also, to observe the scaling benefits of the Verlet scheme, you have to get involved with using OpenMP as the core count gets higher, since the whole point is that it permits more than one core to share the work of a domain, and the (short-ranged part of the) group scheme hasn't been implemented to do that. Since you don't mention OpenMP, you're probably not using it ;-) Similarly, the group scheme is unbuffered by default, so it's an apples-and-oranges comparison unless you state what buffer you used there. Cheers, Mark Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at
[gmx-users] Commands to run simulations using multiple GPU's in version 5.0.1
Dear All, I am trying to run NPT simulations using GROMACS version 5.0.1 of a system of size 140k atoms (protein+water systems) with 2 or more GPU's (model=k20); 8 cores (or more); and 1 or more nodes. I am trying to understand how to run simulations using multiple gpus on more than one node. I get the following errors/output when I run the simulation using the following commands:- Note: time-step used = 2 fs and total number of steps = 2 First 4 cases are using single GPU and cases 5-8 are using 2 GPU's. 1. 1 node, 8 cpus, 1 gpu export OMP_NUM_THREADS = 8 command used- mdrun -s topol.tpr -gpu_id 0 Speed - 5.8 ns/day 2. 1 node, 8 cpus, 1 gpu export OMP_NUM_THREADS = 16 command used- mdrun -s topol.tpr -gpu_id 0 Speed - 4.7 ns/day 3. 1 node, 8cpus, 1gpu mdrun -s topol.tpr -ntomp 8 -gpu_id 0 Speed- 5.876 ns/day 4. 1 node, 8cpus, 1gpu mdrun -s topol.tpr -ntomp 16 -gpu_id 0 Fatal Error: Environment variable OMP_NUM_THREADS (8) and the number of threads requested on the command line (16) have different values. Either omit one, or set them both to the same value. Question for 3 and 4 : Do I need to always use OMP_NUM_THREADS or is there a way ntomp overwrites the environment settings? 5. 1 node, 8cpus , 2gpus export OMP_NUM_THREADS = 8 mpirun -np 2 mdrun -s topol.tpr -pin on -gpu_id 01 Speed - 4.044 ns/day 6. 2 nodes, 8cpus , 2 gpus export OMP_NUM_THREADS = 8 mpirun -np 2 mdrun -s topol.tpr -pin on -gpu_id 01 Speed - 3.0 ns/day Are the commands that I used for 5 and 6 correct? 7. I also used (1node, 8 cpus, 2 gpus) mdrun -s topol.tpr -ntmpi 2 -ntomp 8 -gpu_id 01 but this time I get a fatal error: thread mpi's are requested but gromacs is not compiled with thread MPI. Question: Isn't thread MPI enabled by default? 8. Finally, I recompiled Gromacs without OpenMP and re-ran case 1 but this time there is a fatal error More than 1 OpenMP thread requested, but Gromacs was compiled without OpenMP support. command : mdrun -s topol.tpr (no environment settings) -gpu_id 0 Question: Here again, I assumed thread MPI is enabled by default and I think Gromacs still assumes OpenMp thread settings. Am i doing something wrong here? Thanks in advance for your help -- Siva -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Some Scaling of 5.0 Results
Mark, Thanks for sharing. Since the best way to write code that scales well is to write code that runs slowly, we generally prefer to look at raw ns/day. Choosing between perfect scaling of implementation A at 10 ns/day and imperfect scaling of implementation B starting at 50 ns/day is a no-brainer, but only if you know the throughput. Though from an end user point of view, CPU hours are things not to be wasted, so efficiency tends to be more important. I'd also be very suspicious of your single-core result, based on your super-linear scaling. When using a number of cores smaller than a node, you need to take care to pin that thread (mdrun -pin on), and not having other processes also running on that core/node. If that result is noisy because it ran into different other stuff over time, then every scaling data point is affected. Had been wondering about that for awhile and had not looked into it. Did think that might be the reason for the super scaling, will get back to testing that (and all the other options) once this quarter is over. As I am sure you are aware, end of quarter equals very heavy loads on clusters as people try to use up their quota. Also, to observe the scaling benefits of the Verlet scheme, you have to get involved with using OpenMP as the core count gets higher, since the whole point is that it permits more than one core to share the work of a domain, and the (short-ranged part of the) group scheme hasn't been implemented to do that. Since you don't mention OpenMP, you're probably not using it ;-) Yep, that would be right. Another option that I need to look into. This was meant to be a starting point, basic system, simple settings, then work through the other various options that I knew someone would pipe up with :) and that I had ignored. Also need to get a script written to automate this scaling testing, making it easier and faster to test all the various options that can be used. Similarly, the group scheme is unbuffered by default, so it's an apples-and-oranges comparison unless you state what buffer you used there. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Some Scaling of 5.0 Results
Szilard, thanks for the comments and thoughts. What was your benchmarking procedure on core counts that represent less than a full socket? As a starting point, I simply used the same settings for everything. Besides the thread affinity issue mentioned by Mark, clock frequency scaling (boost) can also distort performance plots. You will observe artificially high performance on small core counts making the scaling inherently worse - unless this is explicitly turned off in the BIOS/firmware. This can be further enhanced by the low cache traffic when only partially using a multicore CPU. These are both artificial effects that you won't see in real-world runs - unless leaving a bunch of cores empty. There is no single right way to avoid these issues, there certainly are ways to present data in a less than useful manner - especially when it comes to scaling plots. A simple way of avoiding such issues and eliminating the potential for incorrect strong scaling plots is to start from at least a socket (or node). Otherwise, IMO the 8 threads data points on your plot make sense only if you show strong scaling to multiple sockets/nodes by using the same amount of threads per socket as you started with, leaving the rest of the cores free. Fair enough. What run configuration did you use for Verlet on single node? With the Verlet scheme no domain decomposition, that is multithreding-only (OpenMP) runs are typically more efficient than using domain-decomposition. This is typically true up to a full socket and quite often even across two Intel sockets. Same used as for all other options, it had DD on. Added to the list. Did you tune the PME performance, i.e. the number of separate PME ranks? Not as of yet. With 4.6, my system, this same cluster etc I found that using -npme 0 provided the best scaling and through put speed so that is what I used here as a starting point. Did you use nstlist=40 for all Verlet data points? That may not be optimal across all node counts, especially on less than two nodes, but of course that's hard to tell without trying! Yes, used the same setting across all. Will add that to the options to explore. Finally, looking at octanol Verlet plot, especially in comparison with the water plot, what's strange is that the scaling efficiency is much worse than with water and varies quite greatly between neighboring data points. This indicates that something was not entirely right with those runs. Yes, I suspected as much too, but due to time constraints have not gone back to look at them again, yet. I suspect there is probably a load issue that is skewing those results down, they got split across nodes or something like that. Supercomputer is currently rather heavily loaded. Thanks for the comments, and I will get back with some more thorough results next month. If there is anything else that you would be interested in knowing, options to look at and how it impacts things, let me know and I will look into those too. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Some Scaling of 5.0 Results
On Tue, Sep 23, 2014 at 1:32 AM, Dallas Warren dallas.war...@monash.edu wrote: Mark, Thanks for sharing. Since the best way to write code that scales well is to write code that runs slowly, we generally prefer to look at raw ns/day. Choosing between perfect scaling of implementation A at 10 ns/day and imperfect scaling of implementation B starting at 50 ns/day is a no-brainer, but only if you know the throughput. Though from an end user point of view, CPU hours are things not to be wasted, so efficiency tends to be more important. If the objective is maximizing science per CPU cycle, that's typically proportional to ns/day. On the same amount of hardware, running at 100% efficiency for 40 ns/day is worse than 80% efficiency for 50 ns/day. If you can afford to wait for the result, you could maybe run the latter on less hardware at 100% efficiency for 62.5 ns/day. You have to know the throughput to choose well between any of the above - and once you know where it is maximized, you don't really need to know the efficiency. I'd also be very suspicious of your single-core result, based on your super-linear scaling. When using a number of cores smaller than a node, you need to take care to pin that thread (mdrun -pin on), and not having other processes also running on that core/node. If that result is noisy because it ran into different other stuff over time, then every scaling data point is affected. Had been wondering about that for awhile and had not looked into it. Did think that might be the reason for the super scaling, will get back to testing that (and all the other options) once this quarter is over. As I am sure you are aware, end of quarter equals very heavy loads on clusters as people try to use up their quota. Sure. However, there's only your own conscience stopping you asking for a whole node and using only one core, for example. Mark Also, to observe the scaling benefits of the Verlet scheme, you have to get involved with using OpenMP as the core count gets higher, since the whole point is that it permits more than one core to share the work of a domain, and the (short-ranged part of the) group scheme hasn't been implemented to do that. Since you don't mention OpenMP, you're probably not using it ;-) Yep, that would be right. Another option that I need to look into. This was meant to be a starting point, basic system, simple settings, then work through the other various options that I knew someone would pipe up with :) and that I had ignored. Also need to get a script written to automate this scaling testing, making it easier and faster to test all the various options that can be used. Similarly, the group scheme is unbuffered by default, so it's an apples-and-oranges comparison unless you state what buffer you used there. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
