Re: [gmx-users] Set up anti parallel membrane system for CompEL simulation
Am 04.05.20 um 23:21 schrieb Jochen Hub: Am 04.05.20 um 21:33 schrieb Zheng Ruan: Hi, I'm trying to setup an antiparallel membrane system for CompEL simulation. It is relatively straightforward to convert an existing single membrane system to a parallel system by using # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro However, is there an easy way to invert one of the membrane protein configurations along with the membrane, water and ions? You could try: gmx editconf -rotate 90 0 0 Sorry, I meant of course editconf -rotate 180 0 0 You probably have to combine this with an editconf -translate, together with a manual extension of the box by 1-2 Angstroem to avoid overlapping water molecules at the box edge. Jochen Cheers, Jochen Thanks, Zheng -- --- Prof. Dr. Jochen Hub Theoretical Biophysics Group Department of Physics, Saarland University Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany Phone: +49 (0)681 302-2740 https://biophys.uni-saarland.de/ --- -- 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] Set up anti parallel membrane system for CompEL simulation
Am 04.05.20 um 21:33 schrieb Zheng Ruan: Hi, I'm trying to setup an antiparallel membrane system for CompEL simulation. It is relatively straightforward to convert an existing single membrane system to a parallel system by using # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro However, is there an easy way to invert one of the membrane protein configurations along with the membrane, water and ions? You could try: gmx editconf -rotate 90 0 0 Cheers, Jochen Thanks, Zheng -- --- Prof. Dr. Jochen Hub Theoretical Biophysics Group Department of Physics, Saarland University Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany Phone: +49 (0)681 302-2740 https://biophys.uni-saarland.de/ --- -- 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] 2020.1: comm broken with -update gpu -bonded gpu ?
Hi Magnus and Justin, Am 23.03.20 um 13:52 schrieb Magnus Lundborg: > Hi Jochen, > > Have you tested if this happens with -update cpu? Perhaps it's the bonded on GPU that's the problem, unrelated to updating. The problem only appears with -update gpu, not with -update cpu. I didn't see a > Redmine issue yet. Could you make one? I tried, but I seem to lack permissions: On https://redmine.gromacs.org/projects/gromacs/issues/new I get "You are not authorized to access this page." Did I miss something here? Thanks, Jochen Am 23.03.20 um 13:52 schrieb Magnus Lundborg: Hi Jochen, Have you tested if this happens with -update cpu? Perhaps it's the bonded on GPU that's the problem, unrelated to updating. I didn't see a Redmine issue yet. Could you make one? Cheers, Magnus On 2020-03-19 18:01, Jochen Hub wrote: Hi developers, I am running a simple DPPC membrane (Berger force field, PME, 1nm cutoff, 4fs time step, all standard) with 2020.1 and comm-mode = Linear nstcomm = 100 comm-grps = DPPC water ; OR System but the membrane rapidly drifts along the z direction: approx. once across the box per 100ps, and accelerating over time. This happens only with mdrun -update gpu -bonded gpu but not with mdrun -update gpu -bonded cpu (no spelling mistake) (with a GTX 1070Ti). Also no problems with 2018.6 or 2019.6. Seems like the center of mass motion removal is broken when doing both *bonded and updating* on the GPU. Is this issue known? Cheers, Jochen -- ------- Prof. Dr. Jochen Hub Theoretical Biophysics Group Department of Physics, Saarland University Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany Phone: +49 (0)681 302-2740 https://biophys.uni-saarland.de/ --- -- 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] 2020.1: comm broken with -update gpu -bonded gpu ?
Hi developers, I am running a simple DPPC membrane (Berger force field, PME, 1nm cutoff, 4fs time step, all standard) with 2020.1 and comm-mode= Linear nstcomm = 100 comm-grps= DPPC water ; OR System but the membrane rapidly drifts along the z direction: approx. once across the box per 100ps, and accelerating over time. This happens only with mdrun -update gpu -bonded gpu but not with mdrun -update gpu -bonded cpu (no spelling mistake) (with a GTX 1070Ti). Also no problems with 2018.6 or 2019.6. Seems like the center of mass motion removal is broken when doing both *bonded and updating* on the GPU. Is this issue known? Cheers, Jochen -- --- Prof. Dr. Jochen Hub Theoretical Biophysics Group Department of Physics, Saarland University Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany Phone: +49 (0)681 302-2740 https://biophys.uni-saarland.de/ --- -- 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] Performance with Epyc Rome
Dear Gromacs users, does someone already have experience with the new AMD Epyc Rome? Can we expect that 4 Epyc Cores per Nvidia RTX 2080 on a CPU/GPU node is sufficient for common simulations (as one would expect with an common Intel Xeon)? Many thanks, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] wham analysis
Hi, you can also use the pullf output for WHAM (option -if), this may be easier. Cheers, Jochen Am 26.08.19 um 12:59 schrieb Negar Parvizi: Dear all,I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my file which is protein-ligand complex. The pulling force was in Y direction. when Umbrella sampling finished, "Wham" couldn't analysis the data because wham is in z direction.what should I do now for wham analysis? how can I change it to Y direction?what justin said: I didn't understand it: "WHAM does not presuppose the axis or vector; it does what you tell it. If you're referring to the x-axis label in the PMF profile being "z," that is just a generic (and perhaps imprecise) label that should be changed to the Greek character xi, per conventional notation." So I decided copy the error: Here is the error: Found 25 tpr and 25 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 12 tpr and pullf files Automatic determination of boundaries... Reading file umbrella0.tpr, VERSION 5.1.4 (single precision) File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N Y], (1 dimensions) Pull group coordinates not expected in pullx files. crd 0) k = 1000 position = 0.840198 Use option -v to see this output for all input tpr files Reading pull force file with pull geometry distance and 1 pull dimensions Expecting these columns in pull file: 0 reference columns for each individual pull coordinate 1 data columns for each pull coordinate With 1 pull groups, expect 2 columns (including the time column) Reading file umbrella71.tpr, VERSION 5.1.4 (single precision) Reading file umbrella98.tpr, VERSION 5.1.4 (single precision) Reading file umbrella111.tpr, VERSION 5.1.4 (single precision) Reading file umbrella119.tpr, VERSION 5.1.4 (single precision) Reading file umbrella139.tpr, VERSION 5.1.4 (single precision) Reading file umbrella146.tpr, VERSION 5.1.4 (single precision) Reading file umbrella157.tpr, VERSION 5.1.4 (single precision) Reading file umbrella180.tpr, VERSION 5.1.4 (single precision) Reading file umbrella202.tpr, VERSION 5.1.4 (single precision) I would appreciate any help Tanks in advance, Negar -- ------- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] OPLS parameters for O2
The O2 model pointed out by David is certainly ok for many applications, but Luca Monticelli did some careful work on testig O2 models. That is worth taking a look as well. Cheers, Jochen Am 10.05.19 um 00:42 schrieb Shadi Fuladi: Hi, I'm trying to test molecular oxygen diffusion in electrolytes using OPLS force field. Is there any O2 parameters tested with OPLS AA forcefield? Thanks, SF -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Detection for best SIMD instructions failed, using SIMD None
Hi developers, cmake is not able to detect that our CPUs support AVX2_256: -- Detecting best SIMD instructions for this CPU -- Detection for best SIMD instructions failed, using SIMD - None This happens on - Arch Linux - Gromacs 2018.6 and 2019.1 - cmake version 3.14.1 - with Intel Xeon E5-2643 v4 and Xeon E-2136 - gcc 8.2.1 When specifying manually cmake -DGMX_SIMD=AVX2_256 all is fine and mdrun runs smoothly with expected performance. Is this the intended behavior? Is there something we should report to find the reason for this behavior? Thank you, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Installation with CUDA on Debian / gcc 6+
Hi Mark, Szilárd, and Åke, many thanks for your help, this fully answers our questions. Cheers, Jochen Am 01.04.19 um 18:28 schrieb Szilárd Páll: On Mon, Apr 1, 2019 at 5:08 PM Jochen Hub wrote: Hi Åke, ah, thanks, we had indeed a CUDA 8.0 on our Debian. So we'll try to install CUA 10.1. But as a side question: Doesn't the supported gcc version strongly depend on the Linux distribution, see here: https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html On paper yes in practice not so much. The officially listed "qualified" combinations are not strict (and hard) requirement-combinations; as long as the CUDA dkms compiles for your kernel and the nvcc works with the gcc compiler you provide it, things will generally work. Kernels or compilers shipped by a distro can deviate enough from others that issues may arise, but those cases are not overly common (as far as I know, though admittedly I don't maintain diverse infrastructure). By the way, your distro is not "qualified" at all ;) -- Szilárd Thanks, Jochen Am 01.04.19 um 16:52 schrieb Åke Sandgren: Use a newer version of CUDA? CUDA 10.1 supports GCC 8. On 4/1/19 4:33 PM, Jochen Hub wrote: Hi all, we try to install Gromacs with CUDA support on a Debian system. Cuda complains about the gcc 6.30 naively installed on Debian, since Cuda supports gcc only until gcc 5. The problem is that Debian removed packages for gcc-5, so installing an older gcc is more tedious. We understand that CUDA support for gcc strongly depends on the Linux Distribution, see https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html Therefore: Is there any workaround to compile Gromacs with CUDA under Debian with a gcc 6+ ? Thanks a lot, Jochen -- ------- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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. -- ------- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Installation with CUDA on Debian / gcc 6+
Hi Åke, ah, thanks, we had indeed a CUDA 8.0 on our Debian. So we'll try to install CUA 10.1. But as a side question: Doesn't the supported gcc version strongly depend on the Linux distribution, see here: https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html Thanks, Jochen Am 01.04.19 um 16:52 schrieb Åke Sandgren: Use a newer version of CUDA? CUDA 10.1 supports GCC 8. On 4/1/19 4:33 PM, Jochen Hub wrote: Hi all, we try to install Gromacs with CUDA support on a Debian system. Cuda complains about the gcc 6.30 naively installed on Debian, since Cuda supports gcc only until gcc 5. The problem is that Debian removed packages for gcc-5, so installing an older gcc is more tedious. We understand that CUDA support for gcc strongly depends on the Linux Distribution, see https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html Therefore: Is there any workaround to compile Gromacs with CUDA under Debian with a gcc 6+ ? Thanks a lot, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Installation with CUDA on Debian / gcc 6+
Hi all, we try to install Gromacs with CUDA support on a Debian system. Cuda complains about the gcc 6.30 naively installed on Debian, since Cuda supports gcc only until gcc 5. The problem is that Debian removed packages for gcc-5, so installing an older gcc is more tedious. We understand that CUDA support for gcc strongly depends on the Linux Distribution, see https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html Therefore: Is there any workaround to compile Gromacs with CUDA under Debian with a gcc 6+ ? Thanks a lot, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Fixing the molecule in the centre of the micelle
Hi, I would use pull-geometry = distance with pull-dim = Y Y Y between the COMs of the micelle and the drug. You can use this already during the energy minimization. I would not use comm-mode = angular, this is meant for other applications. Cheers, Jochen Am 21.11.18 um 19:29 schrieb Alexey Kaa: Dear Gromacs users, I am wondering if you could help with advice. In my simulation I have a drug that is initially put into the centre of a micelle. It tends to drift away towards the micelle-water interface. I would like to run an umbrella sampling simulation in order to get a potential of mean force function from the centre of the micelle (let's assume it is spherical) towards bulk. If I run energy minimisation and the NPT-equillibration the drug molecule (or the micelle) already drifts away to the energetically more favourable position, but obviously these steps must take place as otherwise we have a non-balanced system. I tried to let the molecule equilibrate first and then pull it through the center towards the opposite side of the micelle, but then it rather rotates the whole micelle (even if I apply comm-mode Angular to the micelle-building type of molecule), than goes through the centre. I am wondering if it is possible to fix the centers of mass of both - the drug molecule and also the center of mass of the micelle through the minimisation/equilibration steps before applying the pull-code, but so that the micelle-constructing molecules would equilibrate inside it and also the pressure of water would become uniform outside? Or am I restraining the rotation of the micelle wrongly? API = drug, DLiPC = phospholipids making a micelle. ; mode for center of mass motion removal comm-mode= Angular ; number of steps for center of mass motion removal nstcomm = 1 comm-grps= API DLiPC Thanks, Aleksei -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Non-symmetric PMF across lipid bilayer
rg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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. -- Shreyas Sanjay Kaptan -- 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. -- ------- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] AMBER ff14 RNA force field
Hi all, does anyone know if the recent AMBER ff14 RNA force field by Tana, Piana, Dirks, and Shaw is available for download (www.pnas.org/cgi/doi/10.1073/pnas.1713027115)? Google does not find anything. Many thanks, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] gmx wham (again)
Hi Alex, hi Justin, Am 18.04.18 um 09:17 schrieb Alex: I suppose this question is mostly for Justin... Let me remind what I am dealing with and ask if my idea is correct. I have a rectangular membrane in XY with a pore at (X/2, Y/2) in water and want to get the Gibbs free energy curve for an ion. For this, I have a bunch of starting configurations at (X/2, Y/2) and Z varying between some -z0 and z0. The bias in the "fake" pull mdp is applied as N N Y. Near the membrane, this means the entire plane is sampled, which adds contributions I am not interested in. I want the pore and a small region of the membrane around it, not the membrane, given its propertie So, I applied weak (k=50) in-plane restraint to the ion for each of the sampled configurations -- to keep the sampling region a bit closer to the pore. The results look completely different, but they finally make very good qualitative sense. The ion still walks around within a small disk, but not much -- this tentatively makes me happy. What you want is a /cylindrical flat-bottomed (FB) position restraint/ around the pore, see the manual for "flat-bottomed position restraints". You will make sure that the ion stays close the pore in the xy-plane, and this way you avoid sampling problems at the pore entry and exit. Note that the FB position restraint will change the entropy of the ion in the x-y plane. The entropic correction needed for your PMFs (to remove the contribution form the flat-bottomed restraint) is worked out in Appendix of this paper: http://dx.doi.org/10.1021/acs.jpcb.6b11279 This correction allows you to refer your PMF to a well-defined /area per pore/ or, equivalently, /density of pores/ in the membrane (which sometimes causes a lot of confusion). I would definitely not use a simple (not flat-bottomed) position restraint to restrain the ion near the pore - this may cause artifacts in your PMF. The cylinder-based reaction coordinate (mentioned by Justin) affects how the center of mass of the membrane is computed in Z-direction. Hence, it changes the *reaction coordinate*. But it does *not* affect the sampled xy-plane of the ion. The idea behind the cylinder-based reaction coordinate is to avoid that permeation barriers are smeared out due to membrane undulations. Hence, for a small membrane that hardly undulates, a simple reaction coordinate is probably fine (using pull_coord1_geometry = direction or direction-periodic). I hope this helped. Cheers, Jochen Would you believe the results obtained this way, assuming otherwise proper setup? Thanks, Alex -- ------- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Number of Xeon cores per GTX 1080Ti
Am 03.04.18 um 19:03 schrieb Szilárd Páll: On Tue, Apr 3, 2018 at 5:10 PM, Jochen Hub <j...@gwdg.de> wrote: Am 03.04.18 um 16:26 schrieb Szilárd Páll: On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub <j...@gwdg.de> wrote: benchmar Am 29.03.18 um 20:57 schrieb Szilárd Páll: Hi Jochen, For that particular benchmark I only measured performance with 1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy to do the runs on all possible core counts with increments of 1, but that won't tell a whole lot more than what the performance is of a run using a E5-2620 v4 CPU (with some GPUs) on a certain core count. Even extrapolating from that 2620 to a E5-2630 v4 and expecting to get a good estimate is tricky (given that the latter has 25% more cores for the same TDP!), let alone to any 26xxv4 CPU or the current-gen Skylake chips which have different performance characteristics. As Mark notes, there are some mdp option as well as some system charateristics that will have a strong influence on performance -- if tens of % is something you consider "strong" (some users are fine to be within a 2x ballpark :). What's worth considering is to try to avoid ending up strongly CPU or GPU bound from start. That may admittedly could be a difficult task you would run e.g. both biased MD with large pull groups and all-bonds constraints with Amber FF on large-ish (>100k) systems as well as vanilla MD with CHARMM FF with small-ish (<25k) systems. On the same hardware the former will be more prone to be CPU-bound while the latter will have relatively more GPU-heavy workload. There are many factors that influence the performance of a run and therefore giving a the one right answer to your question is not really possible. What can say is that 7-10 "core-GHz" per fast Pascal GPU is generally sufficient for "typical" protein simulations to run at >=85% of peak. Hi Szilárd, many thanks, this alrady helps me a lot. Just to get it 100% clear what you mean with core-GHz: A 10-core E5-2630v4 with 2.2 GHz would have 22 core-GHz, right? Yes, that's what I was referring to; note that a 2630v4 won't be running at a 2.2 GHz base clock if you run AVX code ;) Okay, I didn't know this. What would be the base clock instead with AVX code? Short version: It's not easy to out details as Intel conveniently omits it from the specs, but it's AFAIK 3-400 MHz lower; also note that "turbo bins" change as a function of cores used (so you can't just benchmark on a few cores leaving the rest idle). Also, the actual clock speed (and overall performance) depend on other factors too so benchmarking and extrapolation might require consider other factors too. Let me know if you are interested in more details. Hi Szilárd, many thanks, that helps a lot! Best, Jochen -- Szilárd Thanks, Jochen Cheers, -- Szilárd On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: Hi, On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub <j...@gwdg.de> wrote: Dear Gromacs community, dear Mark, Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4 cores does not help when using a GTX 1080Ti and PME on the GPU. ... for that particular simulation system. Unfortunately, there were no data points between 4 and 8 CPU cores, hence it was not clear at which #cores the performance actually levels off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon cores does not help, if not having UB potentials, but I don't have a 1080Ti at hand to test for that. Those data points may not have been run. Szilard might have the data - this was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared. So my questions are: - At which number of E5-26XXv4 cores does the performance for common systems level off with a 1080Ti for your test system (GLIC)? - Does the answer depend strongly on the mdp settings (in particular on the LJ cutoff)? Longer LJ cutoff (e.g. from different forcefields) will certainly require more non-bonded work, so then fewer CPU cores would be needed to do the remaining non-offloaded work. However any sweet spot for a particular .tpr would be highly dependent on other effects, such as the ratio of solvent (which typically has less LJ and simpler update) to solute, or the density of dihedral or U-B interactions. And doing pulling or FEP is very different again. The sweet spot for the next project will be elsewhere, sadly. This would help us a lot when choosing the appropriate CPU for a 1080Ti. Many thanks for any suggestions, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany <https://maps.google.com/?q=Justus-von-Liebig-Weg+11,+37077+G%C3%B6ttingen,+Germany=gmail=g> .
Re: [gmx-users] Number of Xeon cores per GTX 1080Ti
Am 03.04.18 um 16:26 schrieb Szilárd Páll: On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub <j...@gwdg.de> wrote: Am 29.03.18 um 20:57 schrieb Szilárd Páll: Hi Jochen, For that particular benchmark I only measured performance with 1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy to do the runs on all possible core counts with increments of 1, but that won't tell a whole lot more than what the performance is of a run using a E5-2620 v4 CPU (with some GPUs) on a certain core count. Even extrapolating from that 2620 to a E5-2630 v4 and expecting to get a good estimate is tricky (given that the latter has 25% more cores for the same TDP!), let alone to any 26xxv4 CPU or the current-gen Skylake chips which have different performance characteristics. As Mark notes, there are some mdp option as well as some system charateristics that will have a strong influence on performance -- if tens of % is something you consider "strong" (some users are fine to be within a 2x ballpark :). What's worth considering is to try to avoid ending up strongly CPU or GPU bound from start. That may admittedly could be a difficult task you would run e.g. both biased MD with large pull groups and all-bonds constraints with Amber FF on large-ish (>100k) systems as well as vanilla MD with CHARMM FF with small-ish (<25k) systems. On the same hardware the former will be more prone to be CPU-bound while the latter will have relatively more GPU-heavy workload. There are many factors that influence the performance of a run and therefore giving a the one right answer to your question is not really possible. What can say is that 7-10 "core-GHz" per fast Pascal GPU is generally sufficient for "typical" protein simulations to run at >=85% of peak. Hi Szilárd, many thanks, this alrady helps me a lot. Just to get it 100% clear what you mean with core-GHz: A 10-core E5-2630v4 with 2.2 GHz would have 22 core-GHz, right? Yes, that's what I was referring to; note that a 2630v4 won't be running at a 2.2 GHz base clock if you run AVX code ;) Okay, I didn't know this. What would be the base clock instead with AVX code? Thanks, Jochen Cheers, -- Szilárd On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: Hi, On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub <j...@gwdg.de> wrote: Dear Gromacs community, dear Mark, Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4 cores does not help when using a GTX 1080Ti and PME on the GPU. ... for that particular simulation system. Unfortunately, there were no data points between 4 and 8 CPU cores, hence it was not clear at which #cores the performance actually levels off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon cores does not help, if not having UB potentials, but I don't have a 1080Ti at hand to test for that. Those data points may not have been run. Szilard might have the data - this was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared. So my questions are: - At which number of E5-26XXv4 cores does the performance for common systems level off with a 1080Ti for your test system (GLIC)? - Does the answer depend strongly on the mdp settings (in particular on the LJ cutoff)? Longer LJ cutoff (e.g. from different forcefields) will certainly require more non-bonded work, so then fewer CPU cores would be needed to do the remaining non-offloaded work. However any sweet spot for a particular .tpr would be highly dependent on other effects, such as the ratio of solvent (which typically has less LJ and simpler update) to solute, or the density of dihedral or U-B interactions. And doing pulling or FEP is very different again. The sweet spot for the next project will be elsewhere, sadly. This would help us a lot when choosing the appropriate CPU for a 1080Ti. Many thanks for any suggestions, Jochen -- ------- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany <https://maps.google.com/?q=Justus-von-Liebig-Weg+11,+37077+G%C3%B6ttingen,+Germany=gmail=g> . Phone: +49-551-39-14189 <+49%20551%203914189> http://cmb.bio.uni-goettingen.de/ --- -- 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_
Re: [gmx-users] Number of Xeon cores per GTX 1080Ti
Am 29.03.18 um 20:57 schrieb Szilárd Páll: Hi Jochen, For that particular benchmark I only measured performance with 1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy to do the runs on all possible core counts with increments of 1, but that won't tell a whole lot more than what the performance is of a run using a E5-2620 v4 CPU (with some GPUs) on a certain core count. Even extrapolating from that 2620 to a E5-2630 v4 and expecting to get a good estimate is tricky (given that the latter has 25% more cores for the same TDP!), let alone to any 26xxv4 CPU or the current-gen Skylake chips which have different performance characteristics. As Mark notes, there are some mdp option as well as some system charateristics that will have a strong influence on performance -- if tens of % is something you consider "strong" (some users are fine to be within a 2x ballpark :). What's worth considering is to try to avoid ending up strongly CPU or GPU bound from start. That may admittedly could be a difficult task you would run e.g. both biased MD with large pull groups and all-bonds constraints with Amber FF on large-ish (>100k) systems as well as vanilla MD with CHARMM FF with small-ish (<25k) systems. On the same hardware the former will be more prone to be CPU-bound while the latter will have relatively more GPU-heavy workload. There are many factors that influence the performance of a run and therefore giving a the one right answer to your question is not really possible. What can say is that 7-10 "core-GHz" per fast Pascal GPU is generally sufficient for "typical" protein simulations to run at >=85% of peak. Hi Szilárd, many thanks, this alrady helps me a lot. Just to get it 100% clear what you mean with core-GHz: A 10-core E5-2630v4 with 2.2 GHz would have 22 core-GHz, right? Thanks, Jochen Cheers, -- Szilárd On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: Hi, On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub <j...@gwdg.de> wrote: Dear Gromacs community, dear Mark, Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4 cores does not help when using a GTX 1080Ti and PME on the GPU. ... for that particular simulation system. Unfortunately, there were no data points between 4 and 8 CPU cores, hence it was not clear at which #cores the performance actually levels off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon cores does not help, if not having UB potentials, but I don't have a 1080Ti at hand to test for that. Those data points may not have been run. Szilard might have the data - this was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared. So my questions are: - At which number of E5-26XXv4 cores does the performance for common systems level off with a 1080Ti for your test system (GLIC)? - Does the answer depend strongly on the mdp settings (in particular on the LJ cutoff)? Longer LJ cutoff (e.g. from different forcefields) will certainly require more non-bonded work, so then fewer CPU cores would be needed to do the remaining non-offloaded work. However any sweet spot for a particular .tpr would be highly dependent on other effects, such as the ratio of solvent (which typically has less LJ and simpler update) to solute, or the density of dihedral or U-B interactions. And doing pulling or FEP is very different again. The sweet spot for the next project will be elsewhere, sadly. This would help us a lot when choosing the appropriate CPU for a 1080Ti. Many thanks for any suggestions, Jochen -- ------- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany <https://maps.google.com/?q=Justus-von-Liebig-Weg+11,+37077+G%C3%B6ttingen,+Germany=gmail=g> . Phone: +49-551-39-14189 <+49%20551%203914189> http://cmb.bio.uni-goettingen.de/ --- -- 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. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-Un
[gmx-users] Number of Xeon cores per GTX 1080Ti
Dear Gromacs community, dear Mark, Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4 cores does not help when using a GTX 1080Ti and PME on the GPU. Unfortunately, there were no data points between 4 and 8 CPU cores, hence it was not clear at which #cores the performance actually levels off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon cores does not help, if not having UB potentials, but I don't have a 1080Ti at hand to test for that. So my questions are: - At which number of E5-26XXv4 cores does the performance for common systems level off with a 1080Ti for your test system (GLIC)? - Does the answer depend strongly on the mdp settings (in particular on the LJ cutoff)? This would help us a lot when choosing the appropriate CPU for a 1080Ti. Many thanks for any suggestions, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Umbrella Sampling - good histogram but no result in profile
ur help. Best regards, Ben -- 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. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] walls with slab of water
Hi, I would use a flat-bottomed position restraint in Z-direction for this purpose, see the Gromacs manual. Cheers, Jochen Am 25.02.18 um 10:17 schrieb Adriano Santana Sanchez: Hi, I am trying to run a SLAB of water with a solute and I want to put a wall on the z axis edge. My problem is how to define *wall_atomtype *in the topology file or in the .itp I am using oplsaa.ff force field with SPC/E water. This is a section of the .mpd: Neighborsearching and short-range nonbonded interactions cutoff-scheme= verlet nstlist = 1 ns_type = grid pbc = xy nwall= 2 *wall_atomtype= W1 W2* wall_type= 10-4 wall_r_linpot= -1 wall_density = 5 5 wall_ewald_zfac = 3 ewald_geometry = 3dc rlist= 1.2 --- ERROR 1 [file topol.top, line 45]: Specified wall atom type W1 is not defined ERROR 2 [file topol.top, line 45]: Specified wall atom type W2 is not defined Thanks, Adriano -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] 2018-beta1: PME/GPU performance question
Hi Szilárd, thank you for the quick reply. Yes, but Urey-Bradley makes only 0.2% of the M-Flops. 99.2% comes from "NxN Ewald Elec. + LJ [F]" or "NxN Ewald Elec. + LJ [V]". Update: I tested Tip3 vs. Charmm-modified Tip3p - not the problem But: The cutoff has a big influence on this effect: This goes so far that, with 4 CPU cores, one gets better performance with 1.4 nm cutoff than with 1.0 nm cutoff (!), see: (New runs, now with Slipids, they also use UB.) # 128 Slipids, 1nm cutoff (poor at small nt) 458.70 <- ! 699.79 8 123.81 10 142.46 12 148.26 # 128 Slipids, 1.4nm cutoff (seems ok) 478.12 <- ! 6 106.48 8 127.24 10 130.26 12 134.25 Something similar happens with a 4x larger system, yet not as extreme. # 512 Slipids, 1nm cutoff (poor at small nt) 421.10 630.67 840.06 1048.01 1251.66 # 512 Slipids, 1.4nm cutoff (seems ok) 420.98 629.98 832.99 1034.68 1236.03 Do you still think this due to bonded work? Thank you, Jochen Am 01.12.17 um 02:26 schrieb Szilárd Páll: Hi Jochen, Short answer: (most likely) it is due to the large difference in the amount of bonded work (relative to the total step time). Does CHARMM36 use UB? Cheers, -- Szilárd On Thu, Nov 30, 2017 at 5:33 PM, Jochen Hub <j...@gwdg.de> wrote: Dear all, I have a question on the performance of the new PME-on-GPU code (2018-beta1) on a Xeon 12-core / GTX 1080 node (Cuda 8, gcc 4.85). With a 84 kAtoms system, I get that the simulations do not benefit from a strong CPU any more. See, using 6 Xeon cores with a GTX 1080 is sufficient. #CPU ns/day 292.88 4 113.18 6 123.36 8 122.62 10 125.76 12 128.84 (This is nice, as we can buy cheap CPUs). (with pinning, pinstride 1, one GPU, -ntmpi 1) On a small system (Charmm36 lipid patch, 30 kAtoms), in contrast, the simulations strongly benefit from more CPU cores. #CPU ns/day 484.11 6 119.24 8 150.84 10 159.63 12 171.30 Is this the expected behaviour? Do you know why? Thank you for any hints, Jochen -- ------- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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. -- ------- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] 2018-beta1: PME/GPU performance question
Dear all, I have a question on the performance of the new PME-on-GPU code (2018-beta1) on a Xeon 12-core / GTX 1080 node (Cuda 8, gcc 4.85). With a 84 kAtoms system, I get that the simulations do not benefit from a strong CPU any more. See, using 6 Xeon cores with a GTX 1080 is sufficient. #CPU ns/day 292.88 4 113.18 6 123.36 8 122.62 10 125.76 12 128.84 (This is nice, as we can buy cheap CPUs). (with pinning, pinstride 1, one GPU, -ntmpi 1) On a small system (Charmm36 lipid patch, 30 kAtoms), in contrast, the simulations strongly benefit from more CPU cores. #CPU ns/day 484.11 6 119.24 8 150.84 10 159.63 12 171.30 Is this the expected behaviour? Do you know why? Thank you for any hints, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Heavy atom - hydrogens bond lengths constraints.
Am 06.05.17 um 15:35 schrieb Dawid das: Dear Gromacs Users, I am a bit anxious about the results I get for my simulation of protein in a box of water using CHARMM 27 force field. Namely, even though I use following options to constrain bond lengths between hydrogen atoms and heavy atoms: constraint_algorithm= lincs constraints = h-bonds lincs_iter = 1 lincs_order = 4 and I do not use define = -DFLEXIBLE so if I understand correctly I do simulate rigid water molecules, right? Anyway, I observe fluctutations of bond lengths between hydrogen atoms and heavy atoms with amplitude up to 0.020 AA. Is this possibly due to the limited precision of xtc files? Do you get the same when reading the trr file? Is this what I can expect? Also, I can clearly see that my water molecules (TIP3P model) are not stiff. Best wishes, Dawid Grabarek -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Strange energy minimization problem with large Martini box
Hi all, we are having a strange problem with an energy minimization of a large box of MARTINI octane. This seems like a Gromacs problem (and not a Martini problem), that's why I ask here. When creating a larger octane box from a small equilibrated octane box with genbox, such as: gmx genconf -f small.gro -nbox 5 5 2 -o large.pdb Then, starting an MD directly from large.pdb works fine, as it should, since small.gro was equilibrated. However, when first doing an energy minimization on large.pdb, then the follow-up MD stops in error due to huge box scalings. This also happens with even larger boxes, such as when using -nbox 6 6 2, -nbox 7 7 2, etc. When creating a smaller box, such as: gmx genconf -f small.gro -nbox 3 3 2 -o not-so-large.pdb (or with -nbox 3 3 2) then no problem occurs after the minimiation. Also, when creating only one layer in Z-direction , such as -nbox 5 5 1 or -nbox 10 10 1, all works fine. Finally: the Fmax in the unstable energy minimization are reasonably low (10E+3 or 10E+2), but also seem a bit unstable, with occational increases to ~10E4. This typically means that there is an issue with the energy minimization. This occurred in 2016.3 and 5.13, in single and double precision, with steep and cg integrator. So seems to be a general problem. Did anyone see something similar? Many thanks, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Setting up simulation system of a protein-detergent complex
Hi Gromacs users, if you want to set up an MD simulation system of a protein-detergent complex, you can find some helpful scripts and suggestions here: http://cmb.bio.uni-goettingen.de/build_pdc.html Cheers, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Pulling/restraints along the radius of gyration
Hi Gromacs users, we have written a little Gromacs extension that allows you to apply harmonic restraints along the radius of gyration of a group of atoms (such as a protein). If you want to use it, here are some more details: http://cmb.bio.uni-goettingen.de/rg_pulling.html Cheers, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] bootstrapping of PMF
Hi Alex,
there is no simple answer to your questions. MD simulations often suffer
from long and unknown autocorrelations. Computing reliable errors from
simulations is difficult since it is not clear which simulation frames
are truly statistically independent. With the bootstrapping of
histograms, you get a reasonable error estimate if
1) Your individual histograms are really independent. This may be
violated, for instance, if the starring position for each window is
similar. For example, if the orientation of peptide with respect to the
surface is was always the same at t=0, or if the internal structure of
the peptide was always the same.
2) Your histograms are sufficiently tight, such that at each position
along the reaction coordinate you have several histograms (such as 5 or
10). If your histograms overlap at +- sigma (or even +-2 sigma), this is
clearly violated.
However, getting individual histograms independent from each other is in
practice easier than getting frames from a single simulation independent
(due to the very long autocorrelation within one simulation). Therefore,
bootstrapping complete histograms is in many cases the best one can do
(if the points 1 and 2 are more or less fulfilled).
Btw: The integrated autocorrelation times in iact.xvg are mainly
important when you enforce a cyclic (or periodic) PMF, in order to
distribute a offset between the right and left end over the PMF (to get
it cyclic). But they are in most cased by no means suitable for getting
the "true" autocorrelation time, which you would need to compute the
error via binning single long simulations (to make sure your bins are
independent).
I hope this helps a bit.
Cheers,
Jochen
Am 09/11/2016 um 17:11 schrieb Alex:
> Dear gromacs user,
>
> I have performed a US simulation to find PMF of a peptide adsorbed to a
> solid surface.
>
> I have already evaluated the result by bootstrapping in gmx WHAM using the
> b-hist method and 600 number of bootstraps and 1200 bins also with
> considering the integrated autocorrelation time into account
>
> Here is the command:
>
> gmx wham -hist Histo.xvg -nBootstrap 600 -bins 1200 -bs-method b-hist
> -bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -min 1.95
> -max 4.7 -ac -o Profile.xvg -zprof0 4.69
>
> And here are the result:
>
> bsProfs.pdf
> https://drive.google.com/open?id=0B_CbyhnbKqQDLWpnQzJ1WmlINXc
>
> bsResult.pdf
> https://drive.google.com/open?id=0B_CbyhnbKqQDRU5kRVdfaU5ObFE
>
> iact.xvg integrated autocorrelation time
> https://drive.google.com/open?id=0B_CbyhnbKqQDOERHTXlrb095VUU
>
> My first question is that if I have well converged PMF result, based on
> above files?
>
> I was also wondering that what exactly I have to be reported later in for
> example a publication and ... ? the normal profile.xvg with out bootstrap
> or this bsProfs.xvg? What is the difference between bsProfs.xvg and the
> normal profile.xvg that we can get from normal gmx WHAM with out
> bootstrapping?
>
> And why the first 130 lines of iact.xvg file have been autocratically
> commented out from the rest?
>
> And finally, do we always and here need to correct all the PMF profile by
> the "$k_{B}T*log[4π(\epsilon)^2]$" factor in which \epsilon is reaction
> coordinate? as been mentioned here:
> Hub, J. S.; de Groot, B. L.; van der Spoel, D.J. Chem. Theory
> Comput.2010,6, 3713-3720
>
> Many thanks for your comments in advance.
>
> Regards,
> Alex
>
--
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
---
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Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
? Best wishes, Dawid Grabarek -- 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. End of gromacs.org_gmx-users Digest, Vol 135, Issue 136 *** -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] New web server for setup of membrane simulation systems
Dear MD community, we have set up a web server that automatically sets up membrane simulation systems containing an arbitrary mixture of different lipids. The server, called MemGen (memgen.uni-goettingen.de) is not restricted to a specific set of lipid types, force fields, or MD software. Instead, MemGen works with any all-atom or united-atom lipid. The user uploads lipids in one of various file formats (pdb, crd, xyz, ml2, gro), and the webserver returns a PDB file of the lipid patch with the requested number relative concentration of the lipids, requested number of water molecules per lipid, and salt content. Counterions are always added. Please give it a try at: http://memgen.uni-goettingen.de/ Happy simulating! The MemGen team at the University of Göttingen -- 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] with 5.0: file INSTALL cannot find gmx
) -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_DEPRECATED_REGISTER -- Performing Test HAS_NO_DEPRECATED_REGISTER - Success -- Configuring done -- Generating done -- Build files have been written to: /home/waxs/opt/gmx/5.03-rotmax -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] with 5.0: file INSTALL cannot find gmx
Am 12/12/14 19:07, schrieb Mark Abraham: Hi, I have seen similar behaviour on interesting setups, e.g. where the same physical file system has different logical locations, but I don't know where the issue is. $(pwd) should be expanded by the shell before cmake sees it, so how a wrong path could get into cmake_install.cmake is a mystery to me. Mark On Fri, Dec 12, 2014 at 6:33 PM, Johnny Lu johnny.lu...@gmail.com wrote: I'm not sure what happened, but so far when i install, i use full path instead of $(pwd) and it was fine for gromacs 4.6 and 5.0, 5.0.2. Thanks, but this is not the issue. As mark says, the shell expands the $(pwd). But I have also before expanded it myself - same error. Jochen -- 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. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] with 5.0: file INSTALL cannot find gmx
Am 12/12/14 19:07, schrieb Mark Abraham: Hi, I have seen similar behaviour on interesting setups, e.g. where the same physical file system has different logical locations, but I don't know where the issue is. $(pwd) should be expanded by the shell before cmake sees it, so how a wrong path could get into cmake_install.cmake is a mystery to me. This may in fact be the issue. Our computing center has some extra-fancy distributed file system. And the webserver we are running is a on a virtual machine, so also some kind of distributed thingie... Hmpf - so is there no solution for that? Jochen Mark On Fri, Dec 12, 2014 at 6:33 PM, Johnny Lu johnny.lu...@gmail.com wrote: I'm not sure what happened, but so far when i install, i use full path instead of $(pwd) and it was fine for gromacs 4.6 and 5.0, 5.0.2. -- 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. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] with 5.0: file INSTALL cannot find gmx
Am 12/12/14 19:40, schrieb Johnny Lu: Oh, and what version of cmake are you using? If that is too old, you can compile a newer version of cmake and then use that. Hey, that was a good hint!! I used 2.8.12.2 before. I just gave it a try with the latest 3.02 - and it worked! So many thanks. Mark, maybe it would be good to suggest a more recent cmake version in general for Gromacs? Best, Jochen On Fri, Dec 12, 2014 at 1:35 PM, Johnny Lu johnny.lu...@gmail.com wrote: maybe ... compile it on the head node of the cluster, and hope it has a local storage? fftpack is slow, and let gromacs build its own fftw3 library is better. I don't know if the fftpack code of gromacs is old. May be Location of where you run cmake/CMakeFiles/CMakeError.log will tell a bit more. On Fri, Dec 12, 2014 at 1:24 PM, Jochen Hub j...@gwdg.de wrote: Am 12/12/14 19:07, schrieb Mark Abraham: Hi, I have seen similar behaviour on interesting setups, e.g. where the same physical file system has different logical locations, but I don't know where the issue is. $(pwd) should be expanded by the shell before cmake sees it, so how a wrong path could get into cmake_install.cmake is a mystery to me. This may in fact be the issue. Our computing center has some extra-fancy distributed file system. And the webserver we are running is a on a virtual machine, so also some kind of distributed thingie... Hmpf - so is there no solution for that? Jochen Mark On Fri, Dec 12, 2014 at 6:33 PM, Johnny Lu johnny.lu...@gmail.com wrote: I'm not sure what happened, but so far when i install, i use full path instead of $(pwd) and it was fine for gromacs 4.6 and 5.0, 5.0.2. -- 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. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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.
