[gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).
Thank you for posting. I also noticed they were using a spherical boundary model; you think using PBC would justify a 50 kJ/mol difference ? As for PME, we wanted to use the classical Ewald summation method, but it turns out that Gromacs hasn't implemented it, yet, for free energy of solvation calculations. Other than that, the only noticeable difference I could find concerns the choice of cutoff radius for ion-water and water-water interactions. -- View this message in context: http://gromacs.5086.x6.nabble.com/Trying-to-replicate-Aqvist-s-results-solvation-free-energy-tp5010407p5010412.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_wham -sym
Hi, I use the g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Thanks for your suggestions in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_wham -sym
On 8/9/13 5:48 AM, Shima Arasteh wrote: Hi, I use the g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Use -zprof0. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs-4.5.5 CPMD QM/MM
Dear All, I am planning to perform a QM/MM calculation of my protein system. Can anybody suggest me whether gromacs-4.5.5 can be patched with any latest version of CPMD? If not, then please suggest me some combination of the gromacs-cpmd versions. I came across this tutorial, but there, both gromacs and cpmd versions are very old. http://www.tougaloo.edu/research/qmmm/ regards, Tarak -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate
Hello David, Thank you again for your reply. It is very interesting idea. Do you mean I can using a grand canonical ensemble to control the surface tension of lipid bilayer by varying its number during my simulations? Is there an existing method in Gromacs to implement so? Or I need to modify the Gromacs code? Could you please give me a clue? And I tried to jump lipids on the 2D periodic graphene layer by adding lipids continuously. Due to the hydrophobicity of lipid tails, the added lipid tails tend to be attached on the graphene layer and form a planar monolayer. But it is not the lipid bilayer I am concerned. If I directly put a periodic lipid bilayer onto the 2D periodic graphene layer, the water molecules between them have no pathway to escape outside. The water permeability through the bilayer is slow in the timescale of MD simulations. The system seems to be time-consuming to find the equilibrium distance between the periodic graphene and the periodic lipid bilayer in MD simulations. Best, Jason --- original message- Message: 2 Date: Thu, 08 Aug 2013 13:41:59 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate Cc: gmx-users@gromacs.org Message-ID: 52038407.7000...@xray.bmc.uu.se Content-Type: text/plain; charset=GB2312 On 2013-08-08 13:17, 朱文鹏 wrote: Hello David, Thank you for your response. Do you mean a finite lipid bilayer on a periodic infinite graphene layer, or a lipid liposome (or a whole spherical cell) on a periodic infinite graphene layer? A 2D periodic graphene layer - which will be an infinite molecule, and then just dump lipids on them, which will form a periodic monolayer. You control the surface tension of the lipids by varying the number. How you would compute the surface tension then is another problem. For the first case, how do you control the surface tension of lipid bilayer? For the second case, I cannot set up a very large spherical cell due to the computational cost. If it is too small, it will be different from the actual situation. Best, Jason --- original message --- Message: 1 Date: Thu, 08 Aug 2013 08:37:15 +0200 From: David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 52033c9b.4040...@xray.bmc.uu.se mailto:52033c9b.4040...@xray.bmc.uu.se Content-Type: text/plain; charset=UTF-8; format=flowed On 2013-08-07 22:50, 朱文鹏 wrote: Dear all, I am trying to set up an all-atom MD simulation to investigate the interaction between lipid bilayer and infinite substrate of graphene or graphene oxide. The edge effects of graphene and graphene oxide are not what I am concerned. The lipid bilayer is placed on the substrate parallelly in the x-y direction. I know the pressure coupling method of surface-tension can control the surface tension in the x-y plane. But it is only for the whole system. The lipid layer and graphene substrate are both infinite in the x-y direction. Can I control the pressure of lipid bilayer and infinite substrate separately? Otherwise, should I change the lipid bilayer to a finite one but still with zero surface tension, or change the graphene substrate to a finite one but without edge effects? How can I remove the edge effects from a finite graphene or GO layer? Do you have any suggestions? I will very appreciate that. Looking forwards to your reply. Why not make a periodic graphene layer (you will have to generate the topology yourself)? You can put anything you like on top of it, and the have pressure coupling only in the normal direction. Best, Jason -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205 tel:%2B46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se http://folding.bmc.uu.se/ -- -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).
never done that calculation myself, so it's hard to say if these differences in the setup may account for such a free energy difference, but I remember one lecture by Phillipe Hünenberger a few years ago when he presented a large compilation of hydration free energies for sodium and the figures changed quite a lot from one simulation to the next, so I wouldn't be surprised if your setup produces a result differing from Aqvist's original report by 50 kJ/mol. I don't think that GROMACS allows you to reproduce the exact setup that was used by Aqvist back then, so if you want to get familiar with the free energy calculations as implemented in GROMACS maybe you should try to reproduce some other more recent calculation using this software, because this is the only way we have guarantees that model systems match each other and that results should match too. cheers Andre On Fri, Aug 9, 2013 at 4:02 AM, Heymman francis.de.lasa...@umontreal.cawrote: Thank you for posting. I also noticed they were using a spherical boundary model; you think using PBC would justify a 50 kJ/mol difference ? As for PME, we wanted to use the classical Ewald summation method, but it turns out that Gromacs hasn't implemented it, yet, for free energy of solvation calculations. Other than that, the only noticeable difference I could find concerns the choice of cutoff radius for ion-water and water-water interactions. -- View this message in context: http://gromacs.5086.x6.nabble.com/Trying-to-replicate-Aqvist-s-results-solvation-free-energy-tp5010407p5010412.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate
On 2013-08-09 14:29, 朱文鹏 wrote: Hello David, Thank you again for your reply. It is very interesting idea. Do you mean I can using a grand canonical ensemble to control the surface tension of lipid bilayer by varying its number during my simulations? Is there an existing method in Gromacs to implement so? Or I need to modify the Gromacs code? Could you please give me a clue? No this isn't implemented and will be quite hard to do. Why don't you try to make a monolayer of the right size using e.g. http://www.membuilder.org and the place this on the graphene using a text editor. Then if you have the right density and you solvate the layer it will stay a monolayer. In principle you could also put a mixture of lipids and water in the box and it will assemble after a while into a monolayer. I guess you want a monolayer, not a bilayer, and hence you will have to remove one of the two generated layers. And I tried to jump lipids on the 2D periodic graphene layer by adding lipids continuously. Due to the hydrophobicity of lipid tails, the added lipid tails tend to be attached on the graphene layer and form a planar monolayer. But it is not the lipid bilayer I am concerned. If I directly put a periodic lipid bilayer onto the 2D periodic graphene layer, the water molecules between them have no pathway to escape outside. The water permeability through the bilayer is slow in the timescale of MD simulations. The system seems to be time-consuming to find the equilibrium distance between the periodic graphene and the periodic lipid bilayer in MD simulations. Best, Jason --- original message- Message: 2 Date: Thu, 08 Aug 2013 13:41:59 +0200 From: David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate Cc: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 52038407.7000...@xray.bmc.uu.se mailto:52038407.7000...@xray.bmc.uu.se Content-Type: text/plain; charset=GB2312 On 2013-08-08 13:17, 朱文鹏 wrote: Hello David, Thank you for your response. Do you mean a finite lipid bilayer on a periodic infinite graphene layer, or a lipid liposome (or a whole spherical cell) on a periodic infinite graphene layer? A 2D periodic graphene layer - which will be an infinite molecule, and then just dump lipids on them, which will form a periodic monolayer. You control the surface tension of the lipids by varying the number. How you would compute the surface tension then is another problem. For the first case, how do you control the surface tension of lipid bilayer? For the second case, I cannot set up a very large spherical cell due to the computational cost. If it is too small, it will be different from the actual situation. Best, Jason --- original message --- Message: 1 Date: Thu, 08 Aug 2013 08:37:15 +0200 From: David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 52033c9b.4040...@xray.bmc.uu.se mailto:52033c9b.4040...@xray.bmc.uu.se mailto:52033c9b.4040...@xray.bmc.uu.se mailto:52033c9b.4040...@xray.bmc.uu.se Content-Type: text/plain; charset=UTF-8; format=flowed On 2013-08-07 22:50, 朱文鹏 wrote: Dear all, I am trying to set up an all-atom MD simulation to investigate the interaction between lipid bilayer and infinite substrate of graphene or graphene oxide. The edge effects of graphene and graphene oxide are not what I am concerned. The lipid bilayer is placed on the substrate parallelly in the x-y direction. I know the pressure coupling method of surface-tension can control the surface tension in the x-y plane. But it is only for the whole system. The lipid layer and graphene substrate are both infinite in the x-y direction. Can I control the pressure of lipid bilayer and infinite substrate separately? Otherwise, should I change the lipid bilayer to a finite one but still with zero surface tension, or change the graphene substrate to a finite one but without edge effects? How can I remove the edge effects from a finite graphene or GO layer? Do you have any suggestions? I will very appreciate that. Looking forwards to your reply. Why not make a periodic graphene layer (you will have to generate the topology yourself)? You can put anything you like on top of it, and the have pressure coupling only in the normal direction. Best, Jason -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205 tel:%2B46184714205 tel:%2B46184714205.
Re: [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k
Hello, Thanks for the reply. I made another even more simple test. I just would like to understand what is going on inside the energy calculation. I have an ALA system. This is the topology file for the bond: [ bonds ] ; ai aj funct r k 1 2 1 1.0100e-01 3.6317e+05 3 4 1 1.0900e-01 2.8451e+05 5 6 1 1.0900e-01 2.8451e+05 5 7 1 1.0900e-01 2.8451e+05 5 8 1 1.0900e-01 2.8451e+05 1 3 1 1.4490e-01 2.8200e+05 3 5 1 1.5260e-01 2.5941e+05 3 9 1 1.5220e-01 2.6527e+05 9 10 1 1.2290e-01 4.7698e+05 From here, I computed manually the bond energy which is : sum (ki*(r_i*r_i)) = 42536.87 (kj/mol) however, when I perform a rerun on the gro file ... this is the bond energy: 2.20074e-01 (kj/mol) What am I missing? Thanks G. From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, August 8, 2013 2:40 AM Subject: Re: [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k On 2013-08-08 01:16, Golshan Hejazi wrote: Hello, I have performed quit a lot of tests and I have some question: I have an amber.crd and amber.top files ... I perform a single step energy calculation with amber , gromacs and cp2k. in all of them I am using amber force field but the point is that in cp2k and amber, I am reading crd and top file directly while in gromacs, i need to convert them to gromacs format. I performed this test for a simple ace-ala-nme system. Lets talk only about the BOND, ANGLE and TORSION energies which are the same in all of these packages. these energy components output are identical in amber and cp2k. However, there is a big difference between them and gromacs: cp2k, amber ... BOND= 0.0206 (kcal/mol) ANGLE=0.3620 (kcal/mol) TORSION=8.1071 (kcal/mol) gromacs BOND=0.14044 (kcal/mol) ANGLE=0.3780 (kcal/mol) TORSION=9.74190 (kcal/mol) The other terms are also different. But lets focus on these because they are the same in all these packages. Now, how did i convert the crd and top file to gromacs fromat? 1- I tried amb2gmx perl script 2- I used ambpdb of amber to generate a pdb file and then pdb2gmx of gromacs to generate the top and gro file for gromacs BOTH of these ways gives different results from each other and also from cp2k and amber! I would really appreciate any help about this problem ... it seems to me there is a bug in amber to gmx file convertors?! it looks like some kind of rounding error, pdb file have limited precision. the force constants you can check yourself. Thanks Golshan -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k
On 8/9/13 10:33 AM, Golshan Hejazi wrote: Hello, Thanks for the reply. I made another even more simple test. I just would like to understand what is going on inside the energy calculation. I have an ALA system. This is the topology file for the bond: [ bonds ] ; aiaj funct r k 1 2 1 1.0100e-01 3.6317e+05 3 4 1 1.0900e-01 2.8451e+05 5 6 1 1.0900e-01 2.8451e+05 5 7 1 1.0900e-01 2.8451e+05 5 8 1 1.0900e-01 2.8451e+05 1 3 1 1.4490e-01 2.8200e+05 3 5 1 1.5260e-01 2.5941e+05 3 9 1 1.5220e-01 2.6527e+05 910 1 1.2290e-01 4.7698e+05 From here, I computed manually the bond energy which is : sum (ki*(r_i*r_i)) = 42536.87 (kj/mol) however, when I perform a rerun on the gro file ... this is the bond energy: 2.20074e-01 (kj/mol) What am I missing? It looks like you're calculating the bonded energy wrong. The energy is calculated from the distance the bond length is from the equilibrium value, not the bond length itself. See the manual for the necessary equation. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GPU + surface
Hello. ¿Have you removed periodicity?. Because you may only be seeing traversal of water molecules among copies of the periodic system. Lucio Montero Ph. D. student Instituto de Biotecnologia, UNAM Mexico El 08/08/13 07:39, Ondrej Kroutil escribió: Dear GMX users. I have done simulation of ions and water near quartz surface (ClayFF) using GPU (GTX580) and Gromacs (4.6.1, single precision, 64 bit, SSE4.1, fftw-3.3.3) and have observed strange behavior of water and ions. Its NVT simulation with freezed surface atoms (see .mdp below) and negative charge on surface (deprotonated silanols), system is overall neutral. I used same mdp for normal CPU simulation and GPU simulation, and just added -testverlet option for GPU simulation. In CPU simulation ions and water behaved as expected (see http://i1315.photobucket.com/albums/t587/Andrew_Twister/cpu-simul_zpscf784b46.png) , but in GPU simulation there was a visible flow of ions toward image of lower surface and all water molecules were oriented with hydrogens facing downward and oxygens oriented upwards (see http://i1315.photobucket.com/albums/t587/Andrew_Twister/gpu-simul_zps2c160ea6.png). It looks like there was an applied electric field but it is not. Do you think there is a problem in initial setup of parameters in mdp file? Or maybe problem of freezing groups? With no freeze situation is better, but there is still visible flow and pairing of same ions (see http://i1315.photobucket.com/albums/t587/Andrew_Twister/gpu-no_freeze_zps72ef3938.png). It look as electrostatics problem. Do you have any hints, please? And sorry if I missed similar topic in mailing list, but I couldn't find anything similar. Ondrej Kroutil integrator = md dt = 0.001 nsteps = 10 comm_mode= linear nstcomm = 1000 nstxout = 0 nstxtcout= 1000 nstvout = 0 nstfout = 0 nstlog = 1000 xtc_precision= 1 nstlist = 10 ns_type = grid rlist= 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 constraints = hbonds constraint_algorithm = lincs lincs_iter = 1 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3dc optimize_fft= yes ; Nose-Hoover temperature coupling Tcoupl = nose-hoover tau_t = 1 tc_grps= system ref_t = 298.15 ; No Pressure ; Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 compressibility = 0 4.6e-5 ref_p = 0 1.0 ; OTHER periodic_molecules = no pbc = xyz ;energygrps = SOL SOH freezegrps = BULK freezedim = Y Y Y gen_vel = yes gen_temp= 298.15 gen_seed= -1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Aw: [gmx-users] Umbrella sampling - position restraints
Thanks Justin, Stephan. I am running both and will post my observations soon. -- View this message in context: http://gromacs.5086.x6.nabble.com/Umbrella-sampling-position-restraints-tp5010405p5010422.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P
Mark, Since I was working with 4.6.2, I built 4.6.3 to see if this was the result of a bug in 4.6.2. It isn't I get the same error with 4.6.3, but that is the version I'll be working with from now on, since it's the latest. Since the problem occurs with both versions, might as well try to fix it in the latest version, right? I compiled 4.6.3 with the following options to include debugging information: cmake .. \ -DCMAKE_TOOLCHAIN_FILE=../cmake/Platform/BlueGeneP-static-XL-C.cmake \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_MPI=ON \ -DCMAKE_C_FLAGS=-O0 -g -qstrict -qarch=450 -qtune=450 \ -DCMAKE_INSTALL_PREFIX=/scratch/bgapps/gromacs-4.6.3 \ -DGMX_CPU_ACCELERATION=None \ -DGMX_THREAD_MPI=OFF \ -DGMX_OPENMP=OFF \ -DGMX_DEFAULT_SUFFIX=ON \ -DCMAKE_PREFIX_PATH=/scratch/bgapps/fftw-3.3.2 \ 21 | tee cmake.log For qarch, I removed the 'd' from the end, so that the double-FPU isn't used, which can cause problems if the data isn't aligned correctly. The -qstrict makes sure certain optimizations aren't performed. It should be superfluous with optimization levels below 3, but I through it in just to be safe, and set -O0. (of course, I think -g turns off all optizations, anyway) On the BG/P, I had to install FFTW3 separately, and that wasn't installed with debugging active, so there are no symbols for FFTW. One of my coworkers wrote a script that converts BG/P core files to stack traces. In all the kernels I've looked at so far (9 out of 64), the stack ends at a vfprintf call. For example: - /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/resolv/res_init.c:414 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/libio/wgenops.c:419 /scratch/pbisbal/build/gromacs-4.6.3/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.c:673 ??:0 /bghome/bgbuild/V1R4M2_200_2010-100508P/ppc/bgp/comm/sys/dcmf/../ccmi/executor/Broadcast.h:83 /bghome/bgbuild/V1R4M2_200_2010-100508P/ppc/bgp/comm/lib/dev/mpich2/src/mpid/dcmfd/src/coll/reduce/reduce_algorithms.c:69 /bghome/bgbuild/V1R4M2_200_2010-100508P/ppc/bgp/comm/lib/dev/mpich2/src/mpid/dcmfd/src/coll/bcast/bcast_algorithms.c:227 /scratch/pbisbal/build/gromacs-4.6.3/src/mdlib/nbnxn_atomdata.c:779 /scratch/pbisbal/build/gromacs-4.6.3/src/mdlib/nbnxn_atomdata.c:762 /scratch/pbisbal/build/gromacs-4.6.3/src/mdlib/nbnxn_atomdata.c:374 /scratch/pbisbal/build/gromacs-4.6.3/src/mdlib/calcmu.c:88 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/mdrun.c:113 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/runner.c:1492 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/genalg.c:467 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/calc_verletbuf.c:266 ../stdio-common/printf_fphex.c:335 ../stdio-common/printf_fphex.c:452 ??:0 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 - Another node with a different stack looks like this: --- /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/libio/genops.c:982 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/string/memcpy.c:159 /scratch/pbisbal/build/gromacs-4.6.3/src/mdlib/ns.c:423 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/runner.c:1646 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/genalg.c:467 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/calc_verletbuf.c:266 ../stdio-common/printf_fphex.c:335 ../stdio-common/printf_fphex.c:452 ??:0 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 --- All the stacks look like one of these two. Is any of this information useful? My coworker, who has a lot of experience developing for Blue Gene/P's, says this looks like an I/O problem, but he doesn't have the time to dig into the Gromacs source code for us. I'm willing to do some digging, but some guidance from someone who know the code well would be very helpful. Prentice On 08/06/2013 08:19 PM, Mark Abraham wrote: That all looks fine so far. The core file processor won't help unless you've compiled with -g. Hopefully cmake -DCMAKE_BUILD_TYPE=Debug will do that, but I haven't actually checked that really works. If not, you might
[gmx-users] Re: Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1
Hi, I just did the simulation with the last version of Gromacs (4.6.3) and it seems that the problem has disappeared!! Regards, Guillaume -- View this message in context: http://gromacs.5086.x6.nabble.com/Mean-Square-Displacement-gromacs-4-5-Vs-gromacs-4-6-1-tp5010317p5010425.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Use pull code to restrain the COM
Hi Justin, Thank you for your quick reply. In Setting A, grompp reports Pull group natoms pbc atom distance at start reference at t=0 0 0 0 1 14623185-0.000 -0.000 -3.268 6.668 6.693 6.492 The values of reference at t=0 are from the .mdp file. They are the COM of pull group 1 calculated by g_traj -ox -com. But I can not understand the values of distance at start. Where does -3.268 come from? If pull group 0, the reference group is set to be 6.668 6.693 6.492, and grompp can calculate the COM of pull group 1, the distance should be 0.0 0.0 0.0 instead of -0.000 -0.000 -3.268. In Setting B, grompp reports Pull group natoms pbc atomdistance at start reference at t=0 0 0 0 1 14623185 -0.000 -0.000 -3.268 0.000 0.000 -3.268 It seems Setting B doesn't agree with Setting A. Then pull-start=yes doesn't have the effect as I guessed. My situation is a bit complicated and challenging. I am simulating the oligomerization of lipo-peptides inside a lipid bilayer. There are several lipo-peptides in the system. Initially I placed them in the water, i.e., outside the bilayer. Then I found it takes too long (at the scale of microseconds even seconds) for them to spontaneously insert into the bilayer and form an oligomer. Then I artificially placed the lipopeptides into the bilayer, and put them together to create an artificial oligomer. I want to see if they can stay there. But obviously the artificial insertion and oligomerization is unfavourable from the viewpoint of energy. So the lipopeptides have a strong tendency to leave the bilayer. Now I want to restrain the COM of each lipopeptide (at least in z direction) for some time, but give them conformational and orientational degrees of freedom as much as possible, to give rise to the possibility that the artificial oligomer can find a favourable conformation and stay there after the removal of restraints. Unfortunately GROMACS can not restrain the COMs of several groups simultaneously. Then in one short simulation (say 100ps), I can only restrain the COM of one lipopeptide and freeze the others (in z direction). The whole process proceeds as: MD (restrain COM of peptide A, freeze BCD) - CG EM - MD (restrain COM of B, freeze ACD) - CG EM - MD (restrain COM of C, freeze ABD) - CG EM - MD (restrain COM of D, freeze ABC) - Next cyle - From my current experience, the EM step is necessary as in MD steps the freezed lipopeptides developed a large amount of strain. If the strain can not get released, the MD runs will explode in several hundreds of picoseconds (GROMACS reports failures of LINCS and eventually segmentation fault, an obvious indication that the system has exploded.) And pull-k1= 50 is indeed very small. The restrained lipopeptides can displace in z direction by a quite large amount in only hundreds of picoseconds. Could you suggest a different approach, or some suggestions to refine this process? Thank you very much. Best Regards Bin 2013/8/9 gmx-users-requ...@gromacs.org Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Aw: [gmx-users] Umbrella sampling - position restraints (lloyd riggs) 2. Use pull code to restrain the COM (Bin Liu) 3. Re: Use pull code to restrain the COM (Justin Lemkul) 4. Re: Trying to replicate Aqvist's results (solvation free energy). (Andr? Farias de Moura) 5. Re: Trying to replicate Aqvist's results (solvation free energy). (Heymman) 6. g_wham -sym (Shima Arasteh) -- Message: 1 Date: Thu, 8 Aug 2013 23:19:59 +0200 (CEST) From: lloyd riggs lloyd.ri...@gmx.ch Subject: Aw: [gmx-users] Umbrella sampling - position restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: trinity-790b128a-a41d-4a6e-87ac-908747401fc1-1375996798996@3capp-gmx-bs33 Content-Type: text/plain; charset=us-ascii An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20130808/fe9e3133/attachment-0001.html -- Message: 2 Date: Thu, 8 Aug 2013 18:43:09 -0400 From: Bin Liu fdusuperstr...@gmail.com Subject: [gmx-users] Use pull code to restrain the COM To: gmx-users@gromacs.org Message-ID: caha8nljjpyduptamu50tzxkhtwd+gkpur87qkcnzwj3v37s...@mail.gmail.com Content-Type:
[gmx-users] segmentation fault on g_protonate
Hi, My heteromolecule structure is missing hydrogens. I did an aminoacids.hdb entry which I suppose being right. When running `g_protonate -s conf.pdb -o prot.pdb` to add the hydrogens happens an segmentation fault. The traceback for 4.6.4-dev-20130808-afc6131 follows. I could add them by any other ways, but g_protonate seems the right way to do. Can you help me to use g_protonate? Program received signal SIGSEGV, Segmentation fault. 0x77b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0, nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:392 392if (ab[i][j].oname == NULL ab[i][j].tp 0) (gdb) bt #0 0x77b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0, nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:392 #1 0x77b22cd7 in add_h_low (pdbaptr=0x7fffc1e8, xptr=0x7fffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440, ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00, bCheckMissing=0, nabptr=0x7fffdf40, abptr=0x7fffdf48, bUpdate_pdba=1, bKeep_old_pdba=1) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:540 #2 0x77b23b66 in add_h (pdbaptr=0x7fffc1e8, xptr=0x7fffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440, ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00, bAllowMissing=1, nabptr=0x7fffdf40, abptr=0x7fffdf48, bUpdate_pdba=1, bKeep_old_pdba=1) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:781 #3 0x77b24080 in protonate (atomsptr=0x7fffceb8, xptr=0x7fffced8, protdata=0x7fffdf30) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:894 #4 0x004020ff in cmain (argc=1, argv=0x7fffe0d8) at /home/peu/Downloads/gromacs/src/kernel/g_protonate.c:195 #5 0x0040224c in main (argc=5, argv=0x7fffe0d8) at /home/peu/Downloads/gromacs/src/kernel/main.c:29 abraços, Pedro Lacerda -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segmentation fault on g_protonate
On 8/9/13 2:35 PM, Pedro Lacerda wrote: Hi, My heteromolecule structure is missing hydrogens. I did an aminoacids.hdb entry which I suppose being right. When running `g_protonate -s conf.pdb -o prot.pdb` to add the hydrogens happens an segmentation fault. The traceback for 4.6.4-dev-20130808-afc6131 follows. I could add them by any other ways, but g_protonate seems the right way to do. Can you help me to use g_protonate? Program received signal SIGSEGV, Segmentation fault. 0x77b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0, nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:392 392if (ab[i][j].oname == NULL ab[i][j].tp 0) (gdb) bt #0 0x77b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0, nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:392 #1 0x77b22cd7 in add_h_low (pdbaptr=0x7fffc1e8, xptr=0x7fffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440, ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00, bCheckMissing=0, nabptr=0x7fffdf40, abptr=0x7fffdf48, bUpdate_pdba=1, bKeep_old_pdba=1) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:540 #2 0x77b23b66 in add_h (pdbaptr=0x7fffc1e8, xptr=0x7fffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440, ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00, bAllowMissing=1, nabptr=0x7fffdf40, abptr=0x7fffdf48, bUpdate_pdba=1, bKeep_old_pdba=1) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:781 #3 0x77b24080 in protonate (atomsptr=0x7fffceb8, xptr=0x7fffced8, protdata=0x7fffdf30) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:894 #4 0x004020ff in cmain (argc=1, argv=0x7fffe0d8) at /home/peu/Downloads/gromacs/src/kernel/g_protonate.c:195 #5 0x0040224c in main (argc=5, argv=0x7fffe0d8) at /home/peu/Downloads/gromacs/src/kernel/main.c:29 Please file a bug report on redmine.gromacs.org. g_protonate has been in varying states of disrepair for years. I hacked a fix a long time ago, but apparently something has broken again. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Use pull code to restrain the COM
On 8/9/13 12:48 PM, Bin Liu wrote: Hi Justin, Thank you for your quick reply. In Setting A, grompp reports Pull group natoms pbc atom distance at start reference at t=0 0 0 0 1 14623185-0.000 -0.000 -3.268 6.668 6.693 6.492 The values of reference at t=0 are from the .mdp file. They are the COM of pull group 1 calculated by g_traj -ox -com. But I can not understand the values of distance at start. Where does -3.268 come from? If pull group 0, the reference group is set to be 6.668 6.693 6.492, and grompp can calculate the COM of pull group 1, the distance should be 0.0 0.0 0.0 instead of -0.000 -0.000 -3.268. True. That seems buggy, but given that what you're doing is generally not recommended, probably no one has really investigated it. In Setting B, grompp reports Pull group natoms pbc atomdistance at start reference at t=0 0 0 0 1 14623185 -0.000 -0.000 -3.268 0.000 0.000 -3.268 It seems Setting B doesn't agree with Setting A. Then pull-start=yes doesn't have the effect as I guessed. It does, but it's probably impacted by incorrect behavior. My situation is a bit complicated and challenging. I am simulating the oligomerization of lipo-peptides inside a lipid bilayer. There are several lipo-peptides in the system. Initially I placed them in the water, i.e., outside the bilayer. Then I found it takes too long (at the scale of microseconds even seconds) for them to spontaneously insert into the bilayer and form an oligomer. Then I artificially placed the lipopeptides into the bilayer, and put them together to create an artificial oligomer. I want to see if they can stay there. But obviously the artificial insertion and oligomerization is unfavourable from the viewpoint of energy. So the lipopeptides have a strong tendency to leave the bilayer. Now I want to restrain the COM of each lipopeptide (at least in z direction) for some time, but give them conformational and orientational degrees of freedom as much as possible, to give rise to the possibility that the artificial oligomer can find a favourable conformation and stay there after the removal of restraints. Unfortunately GROMACS can not restrain the COMs of several groups simultaneously. Then in one short simulation (say 100ps), I can only restrain the COM of one lipopeptide and freeze the others (in z direction). The whole process proceeds as: MD (restrain COM of peptide A, freeze BCD) - CG EM - MD (restrain COM of B, freeze ACD) - CG EM - MD (restrain COM of C, freeze ABD) - CG EM - MD (restrain COM of D, freeze ABC) - Next cyle - From my current experience, the EM step is necessary as in MD steps the freezed lipopeptides developed a large amount of strain. If the strain can not get released, the MD runs will explode in several hundreds of picoseconds (GROMACS reports failures of LINCS and eventually segmentation fault, an obvious indication that the system has exploded.) And pull-k1= 50 is indeed very small. The restrained lipopeptides can displace in z direction by a quite large amount in only hundreds of picoseconds. Could you suggest a different approach, or some suggestions to refine this process? Thank you very much. If you're experiencing such bad forces, I doubt you'll ever get a COM restraint sufficient to counteract the interactions with the membrane. Moreover, even if you restrain the COM to allow the protein to freely interact with the lipids, the magnitude of the forces will probably yield severe artifacts. You need a better method of inserting the peptides. InflateGRO or g_membed are viable options. We used the former in some recent work studying peptide oligomerization in membranes (http://pubs.acs.org/doi/abs/10.1021/bi400562x), and others have applied different methods for different systems. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
