[gmx-users] choice of forcefield
Dear all, I am a beginner to performing simulations and my system consists of protein+ cholesteryl ester +phospholipid and drug. Papers involving lipids are in general united atom, while those involving drug-protein systems are all-atom mostly. Kindly suggest me which of these, all-atom or united atom should I be using for my system. Thanks for your help in advance Yours sincerely, Revathi M.S. Research Scholar Indian Institute of Technology,Madras India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ion mutation in FEP
Dear Users, I have been trying to carry out FEP calculations for a long time for mutation of Glutamine to Aspartic acid using gromacs 4.5.5. Unfortunately, some questions and problems arises during calculations. Here is the question of mine.With glutamine, the protein charge is -12. To neutralize the system, I added 12 Na+ ions. When I mutate GLN to ASP, the charge in state_B is -13. After I run the grompp command, the result says that my State_B topology has -13 charge since I am not including mutation of ion. How can I mutate 1 particular ion to ensure the neutrality of the state_B. How should I exactly modify my topology file to include counter ions for state B. I am including the part of the mutation in topology file at the end of the e-mail. If you could help me, I really appreciate for you time and help. Residue 221 GLN rtp GLN ; q 0.0 2083 N 221 GLN N 894 -0.31 14.0067 ; qtot -4.31 2084 H 221 GLN H 894 0.31 1.008 ; qtot -4 2085 CH1 221 GLN CA 895 0 13.019 ; qtot -4 2086 CH2 221 GLN CB 895 0 14.027 ; qtot -4 2087 CH2 221 GLN CG 895 0 14.027 DUM 0 14.027 ; qtot -4 2088 C 221 GLN CD 896 0.29 12.011 C 0.27 12.011 ; qtot -3.71 2089 O 221 GLN OE1 896 -0.45 15.9994 OM -0.635 15.9994 ; qtot -4.16 2090 NT 221 GLN NE2 896 -0.72 14.0067 OM -0.635 15.9994 ; qtot -4.88 2091 H 221 GLN HE21 896 0.44 1.008 DUM 0 1.008 ; qtot -4.44 2092 H 221 GLN HE22 896 0.44 1.008 DUM 0 1.008 ; qtot -4 2093 C 221 GLN C 897 0.45 12.011 ; qtot -3.55 2094 O 221 GLN O 897 -0.45 15.9994 ; qtot -4 ** [ moleculetype ] ; Name nrexcl NA+Mg 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NA+ 20167 NA NA+ 1 1.0 22.9898 MG2+ 2.0 24.30 500 ; Compound #mols Protein_chain_C 1 FMT 1 SOL 19795 NA 12 -- 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: GPU-based workstation
I've found GTX Titat with 6gb of RAM and 384 bit. The price of such card is equal to the price of the latest TESLA cards. Could it give me better performance in gromacs ? Also assuming that 1 such card need 600 WATT power supply what supply I need for desktop with two such cards? 2013/5/28 Ehud Schreiber schr...@cgen.com I have nothing to contribute regarding the CPUs, but note that last week Nvidia introduced the GTX 780 GPU (a Titan lite), and this week it is expected to introduce the GTX 770 one (probably an overclocked 680). Therefore, disregarding possible price issues, it seems that the GTX 680 may not be the best option. Date: Mon, 27 May 2013 14:14:51 +0400 From: James Starlight jmsstarli...@gmail.commailto: jmsstarli...@gmail.com Subject: Re: Re: Re: [gmx-users] GPU-based workstation To: Discussion list for GROMACS users gmx-users@gromacs.orgmailto: gmx-users@gromacs.org Message-ID: CAALQopymnZm5r+3q4LK_ncM= vots3fvukbeky4k3pk27n2x...@mail.gmail.commailto:CAALQopymnZm5r+3q4LK_ncM= vots3fvukbeky4k3pk27n2x...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Nvidia benchmarks I've found suggestions of using of the two 6 cores CPU for systems with the 2 GPU. Assuming that I'll be using two 680 GTX cards with 256 bits and 4gb ram (not a profesional nvidia cards like TESLA) what CPU's could give me the best performance- 1 i7 of 8 cores or 2 Xeons e5 with 6 cores ? Does it meaningful to use 2 separate CPU's with several nodes each for the 2 GPU's ? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: QM/MM simulations
Thank you. Can you tell me whether there was such a problem in earlier versions? If not, I could use for example version 4.5.7. Because I think it isn't very important at first stage of experiment. Best regards, David -- View this message in context: http://gromacs.5086.x6.nabble.com/QM-MM-simulations-tp5008196p5008577.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] Gromacs for Non biological systems
Look for my papers. At least, two dozens of them are about non-biophysical stuff. Gromacs can. The question is whether you can provide an adequate Hamiltonian to describe your systems involving Al-surface. Dr. Vitaly Chaban On Mon, May 27, 2013 at 10:59 PM, Jeya vimalan jeyavimala...@gmail.comwrote: Dear Collegues, I was pointed to Gromacs to make it work on the non biological systems. My aim is to understand the interaction of Hf precursors on Gamma Alumina surface. But, i do not know yet if gromacs can efficiently handle this. Can someone help me fiding some papers where GROMACS have been used for the non biological system. jeya -- 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] choice of forcefield
In my mind, MARTINI is a decent option to build your particular topology upon. Dr. Vitaly Chaban On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker revthi.san...@yahoo.comwrote: Dear all, I am a beginner to performing simulations and my system consists of protein+ cholesteryl ester +phospholipid and drug. Papers involving lipids are in general united atom, while those involving drug-protein systems are all-atom mostly. Kindly suggest me which of these, all-atom or united atom should I be using for my system. Thanks for your help in advance Yours sincerely, Revathi M.S. Research Scholar Indian Institute of Technology,Madras India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About Compilation error in gromacs 4.6
Dear Justin Thank you for your Previous reply, I have Downloaded gromacs 4.6 I have configured well using the following command cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX=_d and when i Compile using make command I have got following error make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_avx_128_fma_double.c.o] Error 1 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 How to solve the error What Dependencies should I install to solve This Error I Have installed gCC ,g++ compiler and fftw3.3 in My Ubuntu 10.04 OS I have AMD 8 core processor Thanks In Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] choice of forcefield
What other people do? 2013/5/28 Dr. Vitaly Chaban vvcha...@gmail.com In my mind, MARTINI is a decent option to build your particular topology upon. Dr. Vitaly Chaban On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker revthi.san...@yahoo.com wrote: Dear all, I am a beginner to performing simulations and my system consists of protein+ cholesteryl ester +phospholipid and drug. Papers involving lipids are in general united atom, while those involving drug-protein systems are all-atom mostly. Kindly suggest me which of these, all-atom or united atom should I be using for my system. Thanks for your help in advance Yours sincerely, Revathi M.S. Research Scholar Indian Institute of Technology,Madras India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Compilation error in gromacs 4.6
The actual error message is higher up, but my guess would be your compiler in 10.04 is too old to be useful. Per the installation instructions, you will want the latest version of gcc you can get, and ones that came with 10.04 will very likely be wrong or slower than the latest ones. Mark On Tue, May 28, 2013 at 1:39 PM, vidhya sankar scvsankar_...@yahoo.comwrote: Dear Justin Thank you for your Previous reply, I have Downloaded gromacs 4.6 I have configured well using the following command cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX=_d and when i Compile using make command I have got following error make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_avx_128_fma_double.c.o] Error 1 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 How to solve the error What Dependencies should I install to solve This Error I Have installed gCC ,g++ compiler and fftw3.3 in My Ubuntu 10.04 OS I have AMD 8 core processor Thanks In Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] choice of forcefield
On 2013-05-28 14:39, massimo sandal wrote: What other people do? Read literature. Gromacs allows you to choose many. If you need detailed results use an atomistic force field. 2013/5/28 Dr. Vitaly Chaban vvcha...@gmail.com In my mind, MARTINI is a decent option to build your particular topology upon. Dr. Vitaly Chaban On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker revthi.san...@yahoo.com wrote: Dear all, I am a beginner to performing simulations and my system consists of protein+ cholesteryl ester +phospholipid and drug. Papers involving lipids are in general united atom, while those involving drug-protein systems are all-atom mostly. Kindly suggest me which of these, all-atom or united atom should I be using for my system. Thanks for your help in advance Yours sincerely, Revathi M.S. Research Scholar Indian Institute of Technology,Madras India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] About Compilation error in gromacs 4.6
10.04 comes with gcc 4.3 and 4.4 which should both work (we even test them with Jenkins). Still, you should really get a newer gcc, especially if you have an 8-core AMD CPU (= either Bulldozer or Piledriver) both of which are fully supported only by gcc 4.7 and later. Additionally, AFAIK the 2.6.32 kernel is not really optimal for these CPUs. -- Szilárd On Tue, May 28, 2013 at 3:01 PM, Mark Abraham mark.j.abra...@gmail.com wrote: The actual error message is higher up, but my guess would be your compiler in 10.04 is too old to be useful. Per the installation instructions, you will want the latest version of gcc you can get, and ones that came with 10.04 will very likely be wrong or slower than the latest ones. Mark On Tue, May 28, 2013 at 1:39 PM, vidhya sankar scvsankar_...@yahoo.comwrote: Dear Justin Thank you for your Previous reply, I have Downloaded gromacs 4.6 I have configured well using the following command cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX=_d and when i Compile using make command I have got following error make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_avx_128_fma_double.c.o] Error 1 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 How to solve the error What Dependencies should I install to solve This Error I Have installed gCC ,g++ compiler and fftw3.3 in My Ubuntu 10.04 OS I have AMD 8 core processor Thanks In Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Lennard Jones parameters
On 5/28/13 1:01 AM, Ishwor wrote: Dear all I want to study the simulation of Carbonmonoxide in water. I have seen the Lennard Jones parameters, force constant and partial charges of water in the file spce.itp inherent in gromacs but couldnt get the parameters for CO .I will be pleased if anyone provide me the LJ parameters (epsilon and sigma) ,partial charge of Carbon Monoxide.Due to some technical diffculties I have got no access for the published papers. Thanks Having access to the literature will be essential for continuing your work. In any case, doing such a simulation is not as simple as give me the parameters for molecule X. You need to choose a parent force field that will represent your system and obtain or derive compatible parameters. Parameterization is no easy task (although a diatomic molecule should be fairly straightforward), and you need to be very familiar with how the chosen force field works and is derived, information that will require thorough examination of the literature. -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] Re: QM/MM simulations
On 5/28/13 6:03 AM, DavidPO wrote: Thank you. Can you tell me whether there was such a problem in earlier versions? If not, I could use for example version 4.5.7. Because I think it isn't very important at first stage of experiment. I have no idea. Try 4.5.7 and see. If it does work in 4.5.7, please let us know. -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] About Compilation error in gromacs 4.6
On 28.05.2013 13:39, vidhya sankar wrote: cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX=_d please try cmake .. -DGMX_CPU_ACCELERATION=SSE4.1 -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX=_d I remember to have encountered a problem with older gccs and AVX. M. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About Warnings in Mdrun
Thank you Mirco Wahab and Other Gromacs users As you Mailed Me I have compiled gromacs 4.6 I have installed using the command As posted in mail But I have AMD 8 Core black Edition When I run the mdrun I saw a warning Note: file tpx version 73, software tpx version 83 Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, which is better) What is the Meaning of the Above statement ? How to raise the Performance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Warnings in Mdrun
On 5/28/13 11:11 AM, vidhya sankar wrote: Thank you Mirco Wahab and Other Gromacs users As you Mailed Me I have compiled gromacs 4.6 I have installed using the command As posted in mail But I have AMD 8 Core black Edition When I run the mdrun I saw a warning Note: file tpx version 73, software tpx version 83 Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, which is better) What is the Meaning of the Above statement ? The tpx version indicates that you made the .tpr file with an older version than the one you are using to run the simulation. That's not necessarily a problem, but .mdp settings and algorithms change between versions. The second message is related to your problem before - your hardware can handle a better acceleration (AVX) but your compiler is too old to make use of it, so you had to downgrade to SSE4.1. A new compiler will allow you to use the better acceleration. -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] About Warnings in Mdrun
On 28.05.2013 17:11, vidhya sankar wrote: As you Mailed Me I have compiled gromacs 4.6 I have installed using the command As posted in mail But I have AMD 8 Core black Edition When I run the mdrun I saw a warning Note: file tpx version 73, software tpx version 83 Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, which is better) What is the Meaning of the Above statement ? How to raise the Performance 1) The meaning of the above statement: Your machine is a newer AMD FX with a FMA (fused multiply/add) execution unit. Your Gromacs is compiled for older architectures having SSE (streaming SIMD extensions) version 4.1. But you cannt use the AVX unit properly unless you upgrade your gcc compiler to 4.7.x (maybe 4.6.x will work too). The older gcc is not able to not generate the AVX instructions properly. 2) How to raise the performance: The performance difference between AVX and SSE4.1 on an AMF FX 8350 is marginal (I have a 8350 too) and can be ignored for most real world scenarios. The speedup would be 3%-5% with 4.6.1 for now, depending on the scenario (chosen integrator, system size, electrostatics). Much higher performance gains are to be expected by properly configuring your system (cut off, integration method etc.). This is an advanced topic in itself, please read this http://www.gromacs.org/Documentation/Acceleration_and_parallelization and this http://www.gromacs.org/Documentation/Cut-off_schemes Regards M. -- 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] choice of forcefield
Dear Sir, Thank you so much for your reply. To be specific, my system has only four lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was not able to get all atom parameters for these lipids from the lipid book( only united atom parameters were available). So I had resorted to using united atom for the whole system. But I am afraid if I am missing out on some crucial protein-drug interactions because of this united atom consideration. Kindly guide me in this regard. Thank you so much once again. Yours sincerely, Revathi M.S.Research Scholar Indian Institute of Technology Madras India --- On Tue, 28/5/13, David van der Spoel sp...@xray.bmc.uu.se wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] choice of forcefield To: gmx-users@gromacs.org Date: Tuesday, 28 May, 2013, 1:30 PM On 2013-05-28 14:39, massimo sandal wrote: What other people do? Read literature. Gromacs allows you to choose many. If you need detailed results use an atomistic force field. 2013/5/28 Dr. Vitaly Chaban vvcha...@gmail.com In my mind, MARTINI is a decent option to build your particular topology upon. Dr. Vitaly Chaban On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker revthi.san...@yahoo.com wrote: Dear all, I am a beginner to performing simulations and my system consists of protein+ cholesteryl ester +phospholipid and drug. Papers involving lipids are in general united atom, while those involving drug-protein systems are all-atom mostly. Kindly suggest me which of these, all-atom or united atom should I be using for my system. Thanks for your help in advance Yours sincerely, Revathi M.S. Research Scholar Indian Institute of Technology,Madras India -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
[gmx-users] Re: choice of force field -reg
without knowing full details of your simulated system and the goals you pose, I cannot advise anything more definite than I did before. if I were you and my system were yours, I would start with MARTINI FF. I wish you a success in your endeavor. Dr. Vitaly Chaban On Tue, May 28, 2013 at 6:11 PM, Revthi Sanker revthi.san...@yahoo.comwrote: Dear Sir, Thank you so much for your reply. To be specific, my system has only four lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was not able to get all atom paramters for these lipids from the lipid book( only united atom parameters were available). So I had resorted to using united atom for the whole system. But I am afraid if I am missing out on some crucial protein-drug interactions because of this united atom consideration. Kindly guide me in this regard. Thank you so much once again. Yours sincerely, Revathi M.S.Research Scholar Indian Institute of Technology Madras India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: choice of force field -reg
Chaban, why are you advising MARTINI? It is a coarse-grained force field, one should be well aware of the limitations etc. before deciding to choose it, it's not just another force field. 2013/5/28 Dr. Vitaly Chaban vvcha...@gmail.com without knowing full details of your simulated system and the goals you pose, I cannot advise anything more definite than I did before. if I were you and my system were yours, I would start with MARTINI FF. I wish you a success in your endeavor. Dr. Vitaly Chaban On Tue, May 28, 2013 at 6:11 PM, Revthi Sanker revthi.san...@yahoo.com wrote: Dear Sir, Thank you so much for your reply. To be specific, my system has only four lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was not able to get all atom paramters for these lipids from the lipid book( only united atom parameters were available). So I had resorted to using united atom for the whole system. But I am afraid if I am missing out on some crucial protein-drug interactions because of this united atom consideration. Kindly guide me in this regard. Thank you so much once again. Yours sincerely, Revathi M.S.Research Scholar Indian Institute of Technology Madras India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Compilation error in gromacs 4.6
That'll likely work, but whether Vidhya wants to use it depends whether he cares about his simulation performance on this machine. Mark On Tue, May 28, 2013 at 4:05 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 28.05.2013 13:39, vidhya sankar wrote: cmake .. -DCMAKE_INSTALL_PREFIX=/usr/**local/gromacs4.6 -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX=_d please try cmake .. -DGMX_CPU_ACCELERATION=SSE4.1 -DCMAKE_INSTALL_PREFIX=/usr/**local/gromacs4.6 -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX=_d I remember to have encountered a problem with older gccs and AVX. M. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] choice of forcefield
You'll still need to do some reading. If your moieties have never been used in all-atom simulations, you'll have a big task of parameterization, or have to accept some approximation in your model. Even if they have been used, you'll want to read up on how they were parameterized and whether they've been shown to work well. Search the literature! Mark On Tue, May 28, 2013 at 6:12 PM, Revthi Sanker revthi.san...@yahoo.comwrote: Dear Sir, Thank you so much for your reply. To be specific, my system has only four lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was not able to get all atom parameters for these lipids from the lipid book( only united atom parameters were available). So I had resorted to using united atom for the whole system. But I am afraid if I am missing out on some crucial protein-drug interactions because of this united atom consideration. Kindly guide me in this regard. Thank you so much once again. Yours sincerely, Revathi M.S.Research Scholar Indian Institute of Technology Madras India --- On Tue, 28/5/13, David van der Spoel sp...@xray.bmc.uu.se wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] choice of forcefield To: gmx-users@gromacs.org Date: Tuesday, 28 May, 2013, 1:30 PM On 2013-05-28 14:39, massimo sandal wrote: What other people do? Read literature. Gromacs allows you to choose many. If you need detailed results use an atomistic force field. 2013/5/28 Dr. Vitaly Chaban vvcha...@gmail.com In my mind, MARTINI is a decent option to build your particular topology upon. Dr. Vitaly Chaban On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker revthi.san...@yahoo.com wrote: Dear all, I am a beginner to performing simulations and my system consists of protein+ cholesteryl ester +phospholipid and drug. Papers involving lipids are in general united atom, while those involving drug-protein systems are all-atom mostly. Kindly suggest me which of these, all-atom or united atom should I be using for my system. Thanks for your help in advance Yours sincerely, Revathi M.S. Research Scholar Indian Institute of Technology,Madras India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 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: Re: [gmx-users] GPU-based workstation
Dear all, As far as I understand, the OP is interested in hardware for *running* GROMACS 4.6 rather than developing code. or running LINPACK. To get best performance it is important to use a machine with hardware balanced for GROMACS' workloads. Too little GPU resources will result in CPU idling; too much GPU resources will lead to the runs being CPU or multi-GPU scaling bound and above a certain level GROMACS won't be able to make use of additional GPUs. Of course, the balance will depend both on hardware and simulation settings (mostly the LJ cut-off used). An additional factor to consider is typical system size. To reach near peak pair-force throughput on GPUs you typically need 20k-40k particles/GPU (depends on the architecture) and throughput drops below these values. Hence, in most cases it is preferred to use fewer and faster GPUs rather than more. Without knowing the budgdet and indented use of the machine it is hard to make suggestions, but I would say for a budget desktop box a quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well. If you're considering dual-socket workstations, I suggest you go with the higher core-count and higher frequency Intel CPUs (6+ cores 2.2 GHz), otherwise you may not see as much benefit as you would expect based on the insane price tag (especially if you compare to an i7 3939K or its IVB successor). Cheers, -- Szilárd On Sat, May 25, 2013 at 1:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote: More RAM the better, and the best I have seen is 4 GPU work station. I can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8 or 10 slot board really holds 8 or 10 GPU's). There's cooling problems though with GPU's, as on a board there packed, so extra cooling things may help not blow a GPU, but I would look for good ones (ask around), as its a video game market and they go for looks even though its in casing? The external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont know performance wise, the onboard GPU, the more RAM the marrier...so yes, normal work stations you can get 4 GPU's for a 300 US$ board, but then the price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests software, not Gromacs, so would be nice to see performance...for a small 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10 minutes real for 1 ns sim, but tried simple large 800 amino, 25,000 solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps eq's Stephan Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr Von: James Starlight jmsstarli...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] GPU-based workstation Dear Dr. Watkins! Thank you for the suggestions! In the local shops I've found only Core i7 with 6 cores (like Core i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores than with 4 cores in case of i7 cpu (assuming that I run simulation in cpu+gpu mode )? Also you've mentioned about 4 PCeI MD. Does it means that modern work-station could have 4 GPU's in one home-like desktop ? According to my current task I suppose that 2 GPU's would be suitable for my simulations (assuming that I use typical ASUS MB and 650 Watt power unit). Have someone tried to use several GPU's on one workstation ? What attributes of MB should be taken into account for best performance on such multi-gpu station ? James 2013/5/25 lloyd riggs lloyd.ri...@gmx.ch There's also these, but 1 chip runs 6K US, they can get performance up to 2.3 teraflops per chip though double percission...but have no clue about integration with GPU's...Intell also sells their chips on PCIe cards...but get only about 350 Gflops, and run 1K US$. http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor http://www.xilinx.com/ They can design them though to fit a PCIe slot and run about the same, but still need the board, ram etc... Mostly just to dream about, they say you can order them with radiation shielding as well...so... Stephan Watkins *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr *Von:* James Starlight jmsstarli...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] GPU-based workstation Dear Gromacs Users! I'd like to build new workstation for performing simulation on GPU with Gromacs 4.6 native cuda support. Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system with SD integrator) Now I'd like to build multi-gpu wokstation. My question - How much GPU would give me best performance on the typical home-like workstation. What
[gmx-users] Re: choice of force field -reg
On 2013-05-28 18:09, Revthi Sanker wrote: Dear Sir, Thank you so much for your reply. To be specific, my system has only four lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was not able to get all atom paramters for these lipids from the lipid book( only united atom parameters were available). So I had resorted to using united atom for the whole system. But I am afraid if I am missing out on some crucial protein-drug interactions because of this united atom consideration. Kindly guide me in this regard. Sorry but you need to check literature and search the web. There are quite some resources out there. You might also look for Jochen Hub's web site. Thank you so much once again. Yours sincerely, Revathi M.S.Research Scholar Indian Institute of Technology Madras India -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Aw: Re: [gmx-users] GPU-based workstation
On Sat, May 25, 2013 at 2:16 PM, Broadbent, Richard richard.broadben...@imperial.ac.uk wrote: I've been running on my Universities GPU nodes these are one E5-xeon (6-cores 12 threads) and have 4 Nvidia 690gtx's. My system is 93 000 atoms of DMF under NVE. The performance has been a little disappointing That sounds like a very imbalanced system for GROMACS, you have essentially 8 GPUs with rather poor PCI-E performance (a board share a single PCI-E bus) and only 12 CPU cores to drive the simulation. ~10ns/day. On my home system using a core i5-2500 and a nvidia 560ti I get 5.4ns/day for the same system. On our HPC system using 32 nodes each with 2 quad-core xeon processors I get 30-40ns/day. That sounds somewhat low if these are all moderately fast CPUs and GPUs. I think that to achieve reasonable performance the system has to be balanced between CPU's and GPU's probably getting 2 high end GPU's and a top end xeon E5 or core i7 would be a good choice. Indeed. Even two GPUs may be too much - unless the CPU in question is a very high end i7 or E5. Cheers, -- Szilárd Richard From: lloyd riggs lloyd.ri...@gmx.chmailto:lloyd.ri...@gmx.ch Reply-To: Discussion users gmx-users@gromacs.orgmailto:gmx-users@gromacs.org Date: Saturday, 25 May 2013 12:02 To: Discussion users gmx-users@gromacs.orgmailto:gmx-users@gromacs.org Subject: Aw: Re: [gmx-users] GPU-based workstation More RAM the better, and the best I have seen is 4 GPU work station. I can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8 or 10 slot board really holds 8 or 10 GPU's). There's cooling problems though with GPU's, as on a board there packed, so extra cooling things may help not blow a GPU, but I would look for good ones (ask around), as its a video game market and they go for looks even though its in casing? The external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont know performance wise, the onboard GPU, the more RAM the marrier...so yes, normal work stations you can get 4 GPU's for a 300 US$ board, but then the price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests software, not Gromacs, so would be nice to see performance...for a small 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10 minutes real for 1 ns sim, but tried simple large 800 amino, 25,000 solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps eq's Stephan Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr Von: James Starlight jmsstarli...@gmail.commailto:jmsstarli...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.orgmailto:gmx-users@gromacs.org Betreff: Re: [gmx-users] GPU-based workstation Dear Dr. Watkins! Thank you for the suggestions! In the local shops I've found only Core i7 with 6 cores (like Core i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores than with 4 cores in case of i7 cpu (assuming that I run simulation in cpu+gpu mode )? Also you've mentioned about 4 PCeI MD. Does it means that modern work-station could have 4 GPU's in one home-like desktop ? According to my current task I suppose that 2 GPU's would be suitable for my simulations (assuming that I use typical ASUS MB and 650 Watt power unit). Have someone tried to use several GPU's on one workstation ? What attributes of MB should be taken into account for best performance on such multi-gpu station ? James 2013/5/25 lloyd riggs lloyd.ri...@gmx.chmailto:lloyd.ri...@gmx.ch There's also these, but 1 chip runs 6K US, they can get performance up to 2.3 teraflops per chip though double percission...but have no clue about integration with GPU's...Intell also sells their chips on PCIe cards...but get only about 350 Gflops, and run 1K US$. http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor http://www.xilinx.com/ They can design them though to fit a PCIe slot and run about the same, but still need the board, ram etc... Mostly just to dream about, they say you can order them with radiation shielding as well...so... Stephan Watkins *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr *Von:* James Starlight jmsstarli...@gmail.commailto:jmsstarli...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.orgmailto:gmx-users@gromacs.org *Betreff:* [gmx-users] GPU-based workstation Dear Gromacs Users! I'd like to build new workstation for performing simulation on GPU with Gromacs 4.6 native cuda support. Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system with SD integrator) Now I'd like to build multi-gpu wokstation. My question - How much GPU would give me best performance on the
Re: [gmx-users] Re: GPU-based workstation
On Tue, May 28, 2013 at 10:14 AM, James Starlight jmsstarli...@gmail.com wrote: I've found GTX Titat with 6gb of RAM and 384 bit. The price of such card is equal to the price of the latest TESLA cards. Nope! Titan: $1000 Tesla K10: $2750 Tesla K20(c): $3000 TITAN is cheaper than any Tesla and the fastest of all NVIDIA GPUs (in most cases). Could it give me better performance in gromacs ? The GROMACS GPU kernels are ~40% faster than on a GTX 680 and ~25% faster than a K20, but when it comes to total performance, the differences will obviously be smaller. Also assuming that 1 such card need 600 WATT power supply what supply I need for desktop with two such cards? Nope. The peak power consumption of a TITAN is 250W and in compute-only applications I doubt it draws more than max 70-80% of that. With GROMACS as the GPU is only busy at most 70-80% of the time, the effective consumption will scale roughly with those numbers. You should use one of the online PSU calculators. 2013/5/28 Ehud Schreiber schr...@cgen.com I have nothing to contribute regarding the CPUs, but note that last week Nvidia introduced the GTX 780 GPU (a Titan lite), and this week it is expected to introduce the GTX 770 one (probably an overclocked 680). Therefore, disregarding possible price issues, it seems that the GTX 680 may not be the best option. Date: Mon, 27 May 2013 14:14:51 +0400 From: James Starlight jmsstarli...@gmail.commailto: jmsstarli...@gmail.com Subject: Re: Re: Re: [gmx-users] GPU-based workstation To: Discussion list for GROMACS users gmx-users@gromacs.orgmailto: gmx-users@gromacs.org Message-ID: CAALQopymnZm5r+3q4LK_ncM= vots3fvukbeky4k3pk27n2x...@mail.gmail.commailto:CAALQopymnZm5r+3q4LK_ncM= vots3fvukbeky4k3pk27n2x...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Nvidia benchmarks I've found suggestions of using of the two 6 cores CPU for systems with the 2 GPU. Assuming that I'll be using two 680 GTX cards with 256 bits and 4gb ram (not a profesional nvidia cards like TESLA) what CPU's could give me the best performance- 1 i7 of 8 cores or 2 Xeons e5 with 6 cores ? Does it meaningful to use 2 separate CPU's with several nodes each for the 2 GPU's ? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Aw: Re: Re: [gmx-users] GPU-based workstation
Dear Dr. Pali, Thank you, Stephan Watkins Gesendet:Dienstag, 28. Mai 2013 um 19:50 Uhr Von:Szilrd Pll szilard.p...@cbr.su.se An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: Re: [gmx-users] GPU-based workstation Dear all, As far as I understand, the OP is interested in hardware for *running* GROMACS 4.6 rather than developing code. or running LINPACK. To get best performance it is important to use a machine with hardware balanced for GROMACS workloads. Too little GPU resources will result in CPU idling; too much GPU resources will lead to the runs being CPU or multi-GPU scaling bound and above a certain level GROMACS wont be able to make use of additional GPUs. Of course, the balance will depend both on hardware and simulation settings (mostly the LJ cut-off used). An additional factor to consider is typical system size. To reach near peak pair-force throughput on GPUs you typically need 20k-40k particles/GPU (depends on the architecture) and throughput drops below these values. Hence, in most cases it is preferred to use fewer and faster GPUs rather than more. Without knowing the budgdet and indented use of the machine it is hard to make suggestions, but I would say for a budget desktop box a quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well. If youre considering dual-socket workstations, I suggest you go with the higher core-count and higher frequency Intel CPUs (6+ cores 2.2 GHz), otherwise you may not see as much benefit as you would expect based on the insane price tag (especially if you compare to an i7 3939K or its IVB successor). Cheers, -- Szilrd On Sat, May 25, 2013 at 1:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote: More RAM the better, and the best I have seen is 4 GPU work station. I can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8 or 10 slot board really holds 8 or 10 GPUs). Theres cooling problems though with GPUs, as on a board there packed, so extra cooling things may help not blow a GPU, but I would look for good ones (ask around), as its a video game market and they go for looks even though its in casing? The external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont know performance wise, the onboard GPU, the more RAM the marrier...so yes, normal work stations you can get 4 GPUs for a 300 US board, but then the price goes way up (3-4000 US for an 8-10 gpu board). RAM ordered abroad is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPUs but only on tests software, not Gromacs, so would be nice to see performance...for a small 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10 minutes real for 1 ns sim, but tried simple large 800 amino, 25,000 solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps eqs Stephan Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr Von: James Starlight jmsstarli...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] GPU-based workstation Dear Dr. Watkins! Thank you for the suggestions! In the local shops Ive found only Core i7 with 6 cores (like Core i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores than with 4 cores in case of i7 cpu (assuming that I run simulation in cpu+gpu mode )? Also youve mentioned about 4 PCeI MD. Does it means that modern work-station could have 4 GPUs in one home-like desktop ? According to my current task I suppose that 2 GPUs would be suitable for my simulations (assuming that I use typical ASUS MB and 650 Watt power unit). Have someone tried to use several GPUs on one workstation ? What attributes of MB should be taken into account for best performance on such multi-gpu station ? James 2013/5/25 lloyd riggs lloyd.ri...@gmx.ch Theres also these, but 1 chip runs 6K US, they can get performance up to 2.3 teraflops per chip though double percission...but have no clue about integration with GPUs...Intell also sells their chips on PCIe cards...but get only about 350 Gflops, and run 1K US. http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor http://www.xilinx.com/ They can design them though to fit a PCIe slot and run about the same, but still need the board, ram etc... Mostly just to dream about, they say you can order them with radiation shielding as well...so... Stephan Watkins *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr *Von:* James Starlight jmsstarli...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] GPU-based workstation Dear Gromacs Users! Id like to build new workstation for performing simulation on GPU with Gromacs 4.6 native cuda support. Recently Ive used such setup with Core i5 cpu and nvidia 670 GTX video and obtain good performance (
[gmx-users] arrange the atoms in sphere
Hello All, Does anybody have any script to arrange the molecules in the sphere? Actually, I need to set up a LDL (has hydrophobic core and monolayer of PC around). Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/arrange-the-atoms-in-sphere-tp5008599.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] arrange the atoms in sphere
Use packmol. On Wed, May 29, 2013 at 1:32 AM, dariush d.mohammady...@gmail.com wrote: Hello All, Does anybody have any script to arrange the molecules in the sphere? Actually, I need to set up a LDL (has hydrophobic core and monolayer of PC around). Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/arrange-the-atoms-in-sphere-tp5008599.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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] subspace overlap
Dear all, I am doing PCA on a 110ns run. When calculating the subspace overlap from independent PCA performed in different time windows, I expect the overlap to be 1 only when the time interval is equal to 110ns, since both covariance matrices are identical. However, I found that from the interval 0-70 forwards (I'm increasing each window in 10ns) the overlap reaches that value. Is this expected? From the rmsd, cosine content and visual inspection of the trajectory I expected small changes from this point till the total time, but not the two matrices being equal... Am I doing something wrong or this may happen? Here is my data set of results: Normalized Shape DT 0.6110.6380-10ns 0.6160.6500-20ns 0.6460.6710-30ns 0.6560.6780-40ns 0.6590.6830-50ns 0.8730.9190-60ns 1.0001.0000-70ns 1.0001.0000-80ns 1.0001.0000-90ns 1.0001.0000-100ns 1.0001.0000-110ns = Ttot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 109, Issue 153
Compiling GROMACS w CUDA 5.0 problem I did this a few days. i will share my how to do. i used gromacs 4.6.1. assuming u have the nvidia gpu also 1.$ tar xfz gromacs-4.6.tgz $ cd gromacs-4.6 $ mkdir build-cmake $ cd build-cmake $sudo apt-get install cmake $ cmake .. $cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda sudo apt-get install libfftw3-dev libfftw3-doc $ CMAKE_PREFIX_PATH=/opt/fftw:/opt/cuda cmake .. $cmake .. -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_mod -DGMX_LIBS_SUFFIX=_mod $ make -j 8$make install $ source /usr/local/gromacs/bin/GMXRC Running the file: give the following input in the mdp file cutoff-scheme = Verlet regards ayesha On Mon, May 27, 2013 at 6:00 PM, gmx-users-requ...@gromacs.org wrote: 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. Entropy (Yulian) 2. Re: g_hbond (maggin) 3. Re: mdrun outputs incorrect resnames (Reid Van Lehn) 4. AMBER99 P450 heme topology (Parker de Waal) 5. Compiling GROMACS w CUDA 5.0 problem (Jernej Zidar) -- Message: 1 Date: Sun, 26 May 2013 05:04:59 -0700 (PDT) From: Yulian zzeppeli...@gmail.com Subject: [gmx-users] Entropy To: gmx-users@gromacs.org Message-ID: 1369569899419-5008547.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Dear Gromacs users, There is a problem with entropy calculations with g_anaeig. I have 3 runs 100 ns each. Entropy for each run (Protein-H) is round 31000 J/mol K (100 ns) If I use trjcat to connect two trajectories it is 26000 J/mol K (200 ns) For three connect trajectories it is round 19000 J/mol K I tried to do some checking: For example, I used 50 ns from one traj and 50 ns from the other in different combinations but it does not change the entropy value significantly. It seems that three runs are not so different. Also there is a problem with calculating of entropy on different machines. The result can be different for different machines (+/- several hundreds of J/mol K for this system) I use gromacs-4.5.6. For all runs I use trjconv -pbc nojump before analysis. Thank you. Yulian -- View this message in context: http://gromacs.5086.x6.nabble.com/Entropy-tp5008547.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Message: 2 Date: Sun, 26 May 2013 07:23:56 -0700 (PDT) From: maggin maggin.c...@gmail.com Subject: [gmx-users] Re: g_hbond To: gmx-users@gromacs.org Message-ID: 1369578236451-5008548.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Hi, Erik Thank you very much!Thank you! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507p5008548.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Message: 3 Date: Sun, 26 May 2013 13:21:55 -0400 From: Reid Van Lehn rvanl...@gmail.com Subject: Re: [gmx-users] mdrun outputs incorrect resnames To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cal_famm2ux_osqtsmmscd_fqgzd+c4cwrptgxen8udro2c4...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Great, thank you that did the trick. My fault for not realizing this earlier. Best, Reid On Sun, May 26, 2013 at 2:12 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: No, the residue names are the those from the .top file. But that's not the same as the moleculetypes. You have to change the residue names in the [ atoms ] section. Cheers, Tsjerk On Sun, May 26, 2013 at 12:57 AM, Mark Abraham mark.j.abra...@gmail.com wrote: AFAIK, the residue names in the mdrun output .gro file are those of the structure file you gave to grompp. Mark On Sun, May 26, 2013 at 12:31 AM, Reid Van Lehn rvanl...@gmail.com wrote: Hello, I am simulating a lipid bilayer and wish to apply position restraints to only a subset of the lipids in the bilayer. Since position restraints are applied to all molecules of the same molecule type, I defined a new molecule type (DOPR) which is identical to my lipid species (DOPC) by copying the lipid itp file, renaming it and renaming the corresponding molecule type. I then manually edited a starting .gro file to change a subset of the DOPC molecules to DOPR, edited my topology, renumbered/reordered, etc. I also recreated the index file to account for the
Re: Re: Re: [gmx-users] GPU-based workstation
Dear Dr. Pall! Thank you for your suggestions! Asumming that I have budget of 5000 $ and I want to build gpu-based desktop on this money. Previously I've used single 4 core i5 with GTX 670 and obtain average 10 ns\day performance for the 70k atoms systems (1.0 cutoffs, no virtual sites , sd integrator). Now I'd like to build system based on 2 hight-end GeForces (e.g like TITAN). Should that system include 2 cpu's for good balancing? (e.g two 6 nodes XEONS with faster clocks for instance could be better for simulations than i7, couldnt it?) What addition properties to the MB should I consider for such system ? James 2013/5/28 lloyd riggs lloyd.ri...@gmx.ch Dear Dr. Pali, Thank you, Stephan Watkins *Gesendet:* Dienstag, 28. Mai 2013 um 19:50 Uhr *Von:* Szilárd Páll szilard.p...@cbr.su.se *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* Re: Re: [gmx-users] GPU-based workstation Dear all, As far as I understand, the OP is interested in hardware for *running* GROMACS 4.6 rather than developing code. or running LINPACK. To get best performance it is important to use a machine with hardware balanced for GROMACS' workloads. Too little GPU resources will result in CPU idling; too much GPU resources will lead to the runs being CPU or multi-GPU scaling bound and above a certain level GROMACS won't be able to make use of additional GPUs. Of course, the balance will depend both on hardware and simulation settings (mostly the LJ cut-off used). An additional factor to consider is typical system size. To reach near peak pair-force throughput on GPUs you typically need 20k-40k particles/GPU (depends on the architecture) and throughput drops below these values. Hence, in most cases it is preferred to use fewer and faster GPUs rather than more. Without knowing the budgdet and indented use of the machine it is hard to make suggestions, but I would say for a budget desktop box a quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well. If you're considering dual-socket workstations, I suggest you go with the higher core-count and higher frequency Intel CPUs (6+ cores 2.2 GHz), otherwise you may not see as much benefit as you would expect based on the insane price tag (especially if you compare to an i7 3939K or its IVB successor). Cheers, -- Szilárd On Sat, May 25, 2013 at 1:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote: More RAM the better, and the best I have seen is 4 GPU work station. I can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8 or 10 slot board really holds 8 or 10 GPU's). There's cooling problems though with GPU's, as on a board there packed, so extra cooling things may help not blow a GPU, but I would look for good ones (ask around), as its a video game market and they go for looks even though its in casing? The external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont know performance wise, the onboard GPU, the more RAM the marrier...so yes, normal work stations you can get 4 GPU's for a 300 US$ board, but then the price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests software, not Gromacs, so would be nice to see performance...for a small 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10 minutes real for 1 ns sim, but tried simple large 800 amino, 25,000 solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps eq's Stephan Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr Von: James Starlight jmsstarli...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] GPU-based workstation Dear Dr. Watkins! Thank you for the suggestions! In the local shops I've found only Core i7 with 6 cores (like Core i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores than with 4 cores in case of i7 cpu (assuming that I run simulation in cpu+gpu mode )? Also you've mentioned about 4 PCeI MD. Does it means that modern work-station could have 4 GPU's in one home-like desktop ? According to my current task I suppose that 2 GPU's would be suitable for my simulations (assuming that I use typical ASUS MB and 650 Watt power unit). Have someone tried to use several GPU's on one workstation ? What attributes of MB should be taken into account for best performance on such multi-gpu station ? James 2013/5/25 lloyd riggs lloyd.ri...@gmx.ch There's also these, but 1 chip runs 6K US, they can get performance up to 2.3 teraflops per chip though double percission...but have no clue about integration with GPU's...Intell also sells their chips on PCIe cards...but get
