Re: [gmx-users] ***using output of dl_poly in gromacs??***
On 2013-06-25 21:52, hamid mosaddeghi wrote: Dear all I did some bio simulation by dl_poly ,is it possible use gromacs for analysis data? Best Of Luck sure,if you can output the sim as e.g. a pdb file with multiple frames/models. Some analysis tools need a gromacs topology file which is easy to make for proteins/nucleic acids. Run a gromacs tutorial if you haven't yet. -- 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
Fw: [gmx-users] ***using output of dl_poly in gromacs??***
Dear David thansk for quick reply, but existed one problem, my system include metal and protein that metal not define in gromacs then writing topology is difficult, how do analysis with gromacs without write toplogy? any suggestion will be appreciated - Forwarded Message - From: David van der Spoel sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Sent: Wednesday, 26 June 2013, 11:10 Subject: Re: [gmx-users] ***using output of dl_poly in gromacs??*** On 2013-06-25 21:52, hamid mosaddeghi wrote: Dear all I did some bio simulation by dl_poly ,is it possible use gromacs for analysis data? Best Of Luck sure,if you can output the sim as e.g. a pdb file with multiple frames/models. Some analysis tools need a gromacs topology file which is easy to make for proteins/nucleic acids. Run a gromacs tutorial if you haven't yet. -- 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/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_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] Intel vs gcc compilers
You're using a real-MPI process per core, and you have six cores per I was using the current setup, which is indeed not fully optimized, just to see how much the speed-up is between intel and gcc compiled. processor. The recommended procedure is to map cores to OpenMP threads, and choose the number of MPI processes per processor (and thus the number of OpenMP threads per MPI process) to maximize performance. See http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multi-level_parallelization.3a_MPI.2fthread-MPI_.2b_OpenMP I have optimized this before. In my experience one only gets a speedup from using openMP at high parrellization (+/-200 particles per PP core) and if I use #mpi = total number of cores AND 2 openMP threads per mpi process. The total number of processes is then double the number of cores, so you are effectively overloading/hyperthreading the cores (and thus the number of particles per PP process is +/- 100). I have a similar experience on a newer, intel based system, although there the advantage already starts at lower parrallelization. I was wondering if openMP is always used in combination with hyperthreading? On the machine from my previous email, using openMP gives the warning: Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. With the gcc compiled version the, using 72 cores\700 particles/PP core this indeed leads a slightly lower performance. However using the intel compiled version the simulations get orders of magnitude slower. Groetnis, Djurre -- 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: Fw: [gmx-users] ***using output of dl_poly in gromacs??***
On 2013-06-26 09:14, hamid mosaddeghi wrote: Dear David thansk for quick reply, but existed one problem, my system include metal and protein that metal not define in gromacs then writing topology is difficult, how do analysis with gromacs without write toplogy? any suggestion will be appreciated for some analysis you do not need it at all. For some analysis you could also leave out the metal (e.g. secondary structure of protein). - Forwarded Message - *From:* David van der Spoel sp...@xray.bmc.uu.se *To:* gmx-users@gromacs.org *Sent:* Wednesday, 26 June 2013, 11:10 *Subject:* Re: [gmx-users] ***using output of dl_poly in gromacs??*** On 2013-06-25 21:52, hamid mosaddeghi wrote: Dear all I did some bio simulation by dl_poly ,is it possible use gromacs for analysis data? Best Of Luck sure,if you can output the sim as e.g. a pdb file with multiple frames/models. Some analysis tools need a gromacs topology file which is easy to make for proteins/nucleic acids. Run a gromacs tutorial if you haven't yet. -- 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 mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. mailto:gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
[gmx-users] Tabulated angles - how to use?
Dear Gmx Users, It is described how to use tabulated bonds/angles/dihedrals in 4.2.13 manual. I wish to use tables with angles table_a1.xvg, table_a2.xvg However it is not described which function to use in [ angles ]. It is said about [ bonds ] function 8 or 9 but no angles... Can anyone tell me please? Steven -- 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] Tabulated angles - how to use?
4.2.13 links table 5.5, which goes over several pages and has these details. Mark On Wed, Jun 26, 2013 at 10:36 AM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, It is described how to use tabulated bonds/angles/dihedrals in 4.2.13 manual. I wish to use tables with angles table_a1.xvg, table_a2.xvg However it is not described which function to use in [ angles ]. It is said about [ bonds ] function 8 or 9 but no angles... Can anyone tell me please? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: Gromac trr analysis, wired interacation
Please keep GROMACS usage questions on the mailing list. If you need to share a file, do it via a file sharing service, rather than hoping an individual will appreciate having it in their inbox unsolicited. On point, do check out the http://www.gromacs.org/Documentation/FAQs, where a link to the solution for your issue exists. Mark -- Forwarded message -- From: Hasni Arsad hasni.ar...@gmail.com Date: Wed, Jun 26, 2013 at 3:48 AM Subject: Gromac trr analysis, wired interacation To: Mark Abraham mark.j.abra...@gmail.com Hi Mark, I am very sorry for sending this question directly to you, I have sent this question to gmx-user discussion but its may rejected because containing image file. I am doing MD for 20ns, image in attachment is a part of trr analysis using VMD. Thank you for your comment in advance Hasni Penang, Malaysia -- 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: QM/MM simulations
Thank you! It's work. But another problem has appeared. Apparently this is some error associated with ORCA connecting: Back Off! I just backed up md.log to ./#md.log.5# Reading file topol.tpr, VERSION 4.6 (single precision) Using 1 MPI thread QM/MM calculation requested. Layer 0 nr of QM atoms 30 QMlevel: CASSCF/STO-3G /home/timofeev/ORCA/orca/home/timofeev/ORCA/orca... orca initialised... Back Off! I just backed up traj.trr to ./#traj.trr.4# Back Off! I just backed up traj.xtc to ./#traj.xtc.4# Back Off! I just backed up ener.edr to ./#ener.edr.4# starting mdrun 'GRowing Old MAkes el Chrono Sweat in water' 2000 steps, 1.0 ps. No information on the calculation given in topol.tpr.ORCAINFO Source code file: /home/timofeev/GROMACS/gromacs-4.6/src/mdlib/qm_orca.c, line: 161 Routine should not have been called: qm_orca.c I couldn't found rather information about it. Please, comment it. Regards, David -- View this message in context: http://gromacs.5086.x6.nabble.com/QM-MM-simulations-tp5008196p5009391.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] Re: QM/MM simulations
On 6/26/13 7:02 AM, DavidPO wrote: Thank you! It's work. But another problem has appeared. Apparently this is some error associated with ORCA connecting: Back Off! I just backed up md.log to ./#md.log.5# Reading file topol.tpr, VERSION 4.6 (single precision) Using 1 MPI thread QM/MM calculation requested. Layer 0 nr of QM atoms 30 QMlevel: CASSCF/STO-3G /home/timofeev/ORCA/orca/home/timofeev/ORCA/orca... orca initialised... Back Off! I just backed up traj.trr to ./#traj.trr.4# Back Off! I just backed up traj.xtc to ./#traj.xtc.4# Back Off! I just backed up ener.edr to ./#ener.edr.4# starting mdrun 'GRowing Old MAkes el Chrono Sweat in water' 2000 steps, 1.0 ps. No information on the calculation given in topol.tpr.ORCAINFO Source code file: /home/timofeev/GROMACS/gromacs-4.6/src/mdlib/qm_orca.c, line: 161 Routine should not have been called: qm_orca.c I couldn't found rather information about it. Please, comment it. Apparently, some additional input file ($BASENAME.ORCAINFO) is required, and is supposed to contain ORCA-specific instructions for the calculation. I don't do QM/MM, so I haven't spent much time looking online for tutorials and such. Perhaps the information at http://wwwuser.gwdg.de/~ggroenh/qmmm.html is useful. Note that $BASENAME should be the .tpr prefix and should not include the .tpr file extension. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] AMBER to GROMACS conversion
On Tuesday, June 25, 2013 8:10 PM, Parker de Waal parker.dewaa...@kzoo.edu wrote: Now I've been able to successfully convert the two .mol2 files into gromacs .itp however I am unsure how to convert the .frcmod file as well. I'm sorry, but while topolbuild does convert *.mol2 files into gromacs *.itp files with AMBER parameters, it does not make use of AMBER files. Therefore, topolbuild 1.3 will not convert the *.frcmod files. You should edit your *.itp file with any text editor to change entries according to what is found in the desired *.frcmod file. I should also note that the output from topolbuild 1.3 requires some text editing to be made compatible with GROMACS versions greater than 4.0.* because the arrangement of parameter files within the GROMACS */share/gromacs/top directory was changed and topolbuild has not been updated for that change. Finally, I need to note that for AMBER forcefields in GROMACS naming of atom types was updated to be the standard AMBER atom type names with release of the GROMACS 4.5.* series, but topolbuild 1.3 does not reflect that change either. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- 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: Tabulated Potentials
O'Neill, David wrote Hello Users, Recently I have been trying to implement the use of tabulated potentials in GROMACS to an system of argon atoms. I run a NVE simulation of 1000 argon atoms and then plot the potential energy from the output. ar.itp : [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.0 1.0 [ atomtypes ] ;name at.num masscharge ptype sigmaepsilon Ar 18 39.94 0.000 A 0.34 0.997 [ nonbond_params ] ; ij func c6 c12 Ar Ar 1 0.340.997 Then I run the same simulation but with tabulated potentials. ar.itp: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.0 1.0 [ atomtypes ] ;name at.num masscharge ptype sigmaepsilon Ar 18 39.94 0.000 A 1.000 1.000 [ nonbond_params ] ; ij func c6 c12 Ar Ar 1 1.0001.000 The mdp file has changes of: xtc-grps = ; Selection of energy groups energygrps = Ar energygrp_table = Ar Ar coulombtype = user vdw-type = user My table file (table_Ar_Ar.xvg) looks like this: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 5.00e-04 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 1.00e-03 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 1.50e-03 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 2.00e-03 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 2.50e-03 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 ... ... 1.00e-01 1.00e+01 1.00e+02 -6.1606800110e+03 -3.6964080066e+05 9.5170456866e+06 1.1420454824e+09 1.005000e-01 9.9502487562e+00 9.9007450311e+01 -5.9790513233e+03 -3.5695828796e+05 8.9641561500e+06 1.0703470030e+09 1.01e-01 9.9009900990e+00 9.8029604941e+01 -5.8036392503e+03 -3.4477064853e+05 8.4458948214e+06 1.0034726520e+09 1.015000e-01 9.8522167488e+00 9.7066174865e+01 -5.6342018047e+03 -3.3305626432e+05 7.9599373058e+06 9.4107633173e+08 1.02e-01 9.8039215686e+00 9.6116878124e+01 -5.4705075446e+03 -3.2179456145e+05 7.5041255756e+06 8.8283830301e+08 1.025000e-01 9.7560975610e+00 9.5181439619e+01 -5.3123350657e+03 -3.1096595506e+05 7.0764553285e+06 8.2846306285e+08 ... ... 1.897500e+00 5.2700922266e-01 2.7773872077e-01 -1.3198906261e-04 -4.1735671970e-04 4.3683833118e-09 2.7626139521e-08 1.898000e+00 5.2687038988e-01 2.7759240774e-01 -1.3178057657e-04 -4.1658770253e-04 4.3545938718e-09 2.7531678852e-08 1.898500e+00 5.2673163023e-01 2.7744621029e-01 -1.3157247463e-04 -4.1582030435e-04 4.3408515750e-09 2.7437565921e-08 1.899000e+00 5.2659294365e-01 2.7730012831e-01 -1.3136475599e-04 -4.1505452131e-04 4.3271562481e-09 2.7343799356e-08 1.899500e+00 5.2645433009e-01 2.7715416167e-01 -1.3115741984e-04 -4.1429034960e-04 4.3135077182e-09 2.7250377793e-08 1.90e+00 5.2631578947e-01 2.7700831025e-01 -1.3095046538e-04 -4.1352778540e-04 4.2999058130e-09 2.7157299872e-08 The potential energy is then plotted, but they are different for each system when they should be the same. I have spent quite some time on this checking the files looking for what I have done wrong, it is clear to me that it might be rather obvious but I just can't see it as I'm too far in. Anyone see my mistakes? Regards, Stream -- gmx-users mailing list gmx-users@
[gmx-users] g__dist calculate the distance of two residues from different loops
Dear， when i keep the ligand in the active site, I use the g_dist calculate the distance of two residues from two different loops. i look the sticks model of the two residues by pymol and find that there is a gap between the two residues. after using g_dist calculate the distance, i look the distance.xvg file and find that the |d|=0. why? In the pymol i can look the gap, but the distance.xvg show the |d|=0. when i remove the ligand and get the md.xtc, i calculate the distance between the two residues the |d|1nm. so i think the ligand can control the Channels opend, this is right or not ? And i only want to show teh |d| lines in the distance.xvg, how can i carry out it ?-- 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__dist calculate the distance of two residues from different loops
On 6/26/13 9:32 AM, aixintiankong wrote: Dear， when i keep the ligand in the active site, I use the g_dist calculate the distance of two residues from two different loops. i look the sticks model of the two residues by pymol and find that there is a gap between the two residues. after using g_dist calculate the distance, i look the distance.xvg file and find that the |d|=0. why? In the pymol i can look the gap, but the distance.xvg show the |d|=0. Have you verified that your index groups actually specify what you think they do? when i remove the ligand and get the md.xtc, i calculate the distance between the two residues the |d|1nm. so i think the ligand can control the Channels opend, this is right or not ? You have a potentially unreliable measurement involved, so I would not conclude anything. Beyond that, interpretation of the outcome is your task, based on your knowledge of the literature and the system at hand. And i only want to show teh |d| lines in the distance.xvg, how can i carry out it ? That's the default behavior when plotting in XmGrace. You only get multiple sets plotted with the -nxy option. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: 1-4 interactions free energy calculations
Thank you both, Michael and Justin, I have found more documentation and examples about expanded ensemble, so I think I want to be more documented before try it. Also, I will also follow Justin’s advice about checking the problem with my charge groups and dd before I continue with the simulations. As soon as I start my tests, I will let you know. Thank you for the guidance, Sonia Aguilera Graduate Assistant Department of Checmical Engineering Universidad de los Andes -- View this message in context: http://gromacs.5086.x6.nabble.com/1-4-interactions-free-energy-calculations-tp5009364p5009398.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] Extending Simulations
Hi everybody, I have a question that relates to reproducibility in Gromacs. If I have a .cpt file from a previous simulation and use that for two simulations using tpbconv, how similar should the temperature graphs etc be? When I use the .edr files to plot various properties, there is significant difference between the two graphs and I am not sure how much is acceptable or expected. Along the same lines, is there any way to get exactly (or as close as possible) same trajectories etc that I am missing out on? I am passing the .cpt file to mdrun but are there other niggling details I should take into consideration? Thank you! -- View this message in context: http://gromacs.5086.x6.nabble.com/Extending-Simulations-tp5009399.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] Extending Simulations
It is not very clear as to what you are trying to do? If you have the final coordinates and velocities from a previous simulation, I would recommend start a simulation using the .gro file and ensuring that you have gen-vel=no in the .mdp file. If you have a well-equilibrated system, then the properties should not vary much. On similar lines, you can stitch multiple .edr files using eneconv. On Wed, Jun 26, 2013 at 3:54 PM, Neha nshafi...@wesleyan.edu wrote: Hi everybody, I have a question that relates to reproducibility in Gromacs. If I have a .cpt file from a previous simulation and use that for two simulations using tpbconv, how similar should the temperature graphs etc be? When I use the .edr files to plot various properties, there is significant difference between the two graphs and I am not sure how much is acceptable or expected. Along the same lines, is there any way to get exactly (or as close as possible) same trajectories etc that I am missing out on? I am passing the .cpt file to mdrun but are there other niggling details I should take into consideration? Thank you! -- View this message in context: http://gromacs.5086.x6.nabble.com/Extending-Simulations-tp5009399.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Extending Simulations
On 6/26/13 4:12 PM, HANNIBAL LECTER wrote: It is not very clear as to what you are trying to do? If you have the final coordinates and velocities from a previous simulation, I would recommend start a simulation using the .gro file and ensuring that you have gen-vel=no in the .mdp file. If you have a well-equilibrated system, then the properties should not vary much. On similar lines, you can stitch multiple .edr files using eneconv. Coordinates and velocities, especially in single precision, are insufficient to preserve the previous simulation ensemble. The .cpt file contains a lot more information, especially related to continuity of thermostats, barostats, etc. On Wed, Jun 26, 2013 at 3:54 PM, Neha nshafi...@wesleyan.edu wrote: Hi everybody, I have a question that relates to reproducibility in Gromacs. If I have a .cpt file from a previous simulation and use that for two simulations using tpbconv, how similar should the temperature graphs etc be? When I use the .edr files to plot various properties, there is significant difference between the two graphs and I am not sure how much is acceptable or expected. Have you seen both of these articles? http://www.gromacs.org/Documentation/Terminology/Reproducibility http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation The initial states should be identical, but the trajectories can quickly diverge, as is the case with any MD simulation. The observed properties, on average, should converge to comparable values. Along the same lines, is there any way to get exactly (or as close as possible) same trajectories etc that I am missing out on? I am passing the .cpt file to mdrun but are there other niggling details I should take into consideration? mdrun -reprod can help in this regard. Performance will likely take a hit, though. What's not clear to me is why you *need* identical trajectories. If you want to produce two identical trajectories, what's the point of running two at all? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Membrane Runs Crashing
Hi everybody, My runs keep crashing despite energy minimisation and fiddling around with nstlist values. I have been looking in the Gromacs manual particularly the interaction ranges in the domain decomposition section, which mentions that simulations can stop with error messages about missing interactions and atoms moving too far. It says the interaction between two and multi body bonded (rmb) is set based on the initial configuration automatically. Is there a way that I could see what Gromacs is using as those values after the simulation crashes? I am thinking of using -rdd to change that number and see whether the simulation is more successful, although it will most likely be slower. Please let me know where I can get that information! I am getting frustrated with all these crashing runs. -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Runs-Crashing-tp5009264p5009402.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] Re: Membrane Runs Crashing
On 6/26/13 8:39 PM, Neha wrote: Hi everybody, My runs keep crashing despite energy minimisation and fiddling around with nstlist values. I have been looking in the Gromacs manual particularly the interaction ranges in the domain decomposition section, which mentions that simulations can stop with error messages about missing interactions and atoms moving too far. It says the interaction between two and multi body bonded (rmb) is set based on the initial configuration automatically. Is there a way that I could see what Gromacs is using as those values after the simulation crashes? Not after the crash, but you can see the initial DD setup in the .log file. I am thinking of using -rdd to change that number and see whether the simulation is more successful, although it will most likely be slower. Worth a shot. Please let me know where I can get that information! I am getting frustrated with all these crashing runs. I seem to recall a similar problem that someone reported a while back. Since CG systems have bonded interactions over longer distances than atomistic simulations, the DD setup may not work quite as well. Either try increasing -rdd or simply decreasing the number of processors you are using to create larger DD cells. Doing so should improve the odds that cells do not resize such that they lose track of bonded information. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs GPU system question
Thanks Mirco, good info, your numbers look quite consistent. The only complicating factor is that your CPUs are overclocked by different amounts, which changes the relative performances somewhat compared to non-overclocked parts. However, let me list some prices to show that the top-of-the line AMD and Intel CPUs are in a different league: - AMD FX-8350 is a ~170 Eur; - i7 3770 ~250-280 Eur; - i7 3930K ~500 Eur. It's pretty obvious that AMD wins in terms of price/performance especially if we also consider motherboards which for AMD tend to be slightly cheaper. AMD can't compete in performance with the 6-core Intel Sandy Bridge, though. Note that the AMD-Intel difference is larger in CPU-only benchmarks (the difference is quite large in the CPU non-bonded kernels). With the non-bondeds offloaded to a GPU the AMD-Intel difference shrinks. I get only 1.3x compared to the 1.6x without GPU on a stock FX-8350 / i7 3930K + a fast enough GPU (50k atoms, PME, vsites, rc=1.0 nm). If we're already at it, note that the new Haswell CPUs will give a pretty serious performance boost once AVX2 kernels are out (wip) and the i7 4770 cost pretty much the same as the 3770. To conclude, for the price conscious I suggest AMD FX-8350, for max performance Intel i7 4770 or 3930K. Regarding Hyper-Threading, in GROMACS it can actually improve performance by up to 25%. This is typically the case when running on a single CPU+GPU or with CPUs only at not very high parallelization. However, HT can often hurt performance as it requires running 2x more threads, e.g. with multiple GPUs it's nearly always better to not use HT and e.g. at 100 atoms/core 50 atoms/thread (with HT) will most probably be slower than 100 atoms/thread. When it comes to GPUs, what's best will very much depend on the simulation settings. GPUs are used as co-processors, so it's always best if they are fast enough to keep up with the host CPU, but it's hard to say which GPU is fast enough for which CPU *in general*. E.g. for a 6-core Intel you'll certainly want a GTX 770/780 or Titan, but if you run with long cut-offs even with these you might get CPU-GPU load imbalance. Note that in general you are better off using fewer and faster GPUs rather than more mainly because the domain-decomposition overhead (when gouring from one to two GPUs) is quite high and also because performance on GPUs deteriorates quickly below 30-40k atoms/GPU. Cheers, -- Szilárd On Sun, Jun 23, 2013 at 12:05 AM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 22.06.2013 22:18, Mare Libero wrote: The vendor I contacted was pushing for one of the high end i7 processors with hyper-threading. But from what I can read, most of the MD software don't make any use of it. So, using a the multi-cores AMD (like your FX-8350) can be a cheaper and more advantageous option. Your vendor is, in my opinion, right. The AMD consumer multicores (Piledriver) aren't actually eight-core cpus, but rather similar to 4 core cpus (they are called 'modules'). For testing a user-defined potential, I once compiled performance figures over a range of actual commodity hardware (available to me). These are all workstations and usually overclocked somehow by the students (but only if there's no crash at all in a year ;-) This is all *without GPU*, only the plain and raw CPU processing power for Gromacs is checked for (last column). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Test case: Two coarse-grained implicit-solvent vesicles bumping into each other SD integrator 480,000 particles Box (110nm)³ User-defined potential (rc=0.8225nm) dt=0.020ps CPU ArchCores ns/day - X6/1090T;3.3GHz SSE26C/6T 19.130 - FX-8350;4.5GHz AVX_FMA 4M/8T 34.175 - i7/2600K;4.2GHz AVX_256 4C/8T 39.073 - i7/3770K;4.4GHz AVX_265 4C/8T 41.931 - i7/3930K;4.2GHz AVX_256 6c/12T 56.891 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - You can see here, for CPU performance, you can't really choose anything different from the 6-core i7/3930K. It costs some bucks more than the 4-core-CPUs but will run significantly faster the time you use it. Most of what we do is protein-protein interactions and protein stability studies with explicit water/ions. One of our projects now has 100,000 atoms in a 100 Ang water box (7,800 protein atoms + 67,000 water). It's difficult to be more specific on the parameters since each project is different, but in general we do not deviate much from a standard NPT run. 10nm box/75K atoms is not very large. I guess you'd use a time step of 0.002 ps and a united atom model + spc or spc/e water? 100ns/day seem possible with any GPU from GTX-660 or higher. If you buy a mighty GPU (Titan), the question will be: can your n-core-CPU saturate such a fast GPU monster? A
[gmx-users] REMD
Hai Sir, I did an REMD simulation for an intrinsically disordered peptide.Then I extracted thousands of conformations(pdb) from trajectory. Now I want to compare experimental Chemical Shifts and NOE distance for the peptide with all these conformations.How can I do this? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
