Re: [gmx-users] g_helixorient help
Hi All, Any suggestions? Thanks. On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi All, I am trying to calculate the angle between the axes of two alpha helices (say A and B) in my simulation. I have separate index files for the residues pertaining to each helix. I calculated the tilt.xvg for both A and B. The output is slightly confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets. What do these correspond to? (Helix A has 34 residues). Similarly for bending_A.xvg How do I go about this? Is this the right way to calculate the relative helix axis angle? Thanks, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] [gmx-developers] Fatal error: cudaStreamSynchronize failed in cu_blockwait_nb
That sounds strange. Does the error happen at step? Assuming the it does occur within the first 10 steps, here are a few things to try: - Run cuda-memcheck mdrun -nsteps 10; - Try running with GMX_EMULATE_GPU env. var. set? This will run the GPU acceleration code-path, but will use CPU kernels (equivalent to the CUDA but slow implementation). - Run with GMX_EMULATE_GPU using valgrind: GMX_EMULATE_GPU=1 valgrind mdrun -nsteps 10 Cheers, -- Szilárd On Thu, Jan 30, 2014 at 11:47 AM, AOWI (Anders Ossowicki) a...@novozymes.com wrote: Thanks for your suggestions! I would not make any assumptions though, but rather try a few things first: - Does the card pass a memtest (sourceforge.net/projects/cudagpumemtest/)? The memtest ran for about an hour with no errors. - Does the installation pass the regressiontests? No. These four complex tests fail, all with the usual error: FAILED. Check mdrun.out, md.log files in nbnxn_pme FAILED. Check mdrun.out, md.log files in nbnxn_rf FAILED. Check mdrun.out, md.log files in nbnxn_rzero FAILED. Check mdrun.out, md.log files in nbnxn_vsite Everything else passes. - Is the error reproducible with other inputs? Yes, so far anything that has caused Gromacs to engage the GPU has failed. Our own runs, the samples from the Gromacs website, and the four tests above. Also note that with the default invocation of mdrun you are attempting to use all cores/hardware threads in your machine (I assume a 2x12-core IVB-E node with HT on). Two Xeon E5-2697V2 processors yes. This is a test server for gauging the potential performance gains of GPGPU with our own runs. We'll stick to a proper CPU-GPU ratio for the performance measurements. This was just me trying to pare it down to the simplest invocation. We have had no trouble using other CUDA-enabled tools on this particular test server. NAMD, for example, works fine. -- Anders Ossowicki -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] [gmx-developers] Fatal error: cudaStreamSynchronize failed in cu_blockwait_nb
Does the error happen at step? Assuming the it does occur within the first 10 steps, here are a few things to try: It happens immediately. As in: $ time mdrun snip real0m3.312s user0m6.768s sys 0m1.968s $ - Run cuda-memcheck mdrun -nsteps 10; A wild backtrace appeared! starting mdrun 'RNASE ZF-1A in water' 10 steps, 0.0 ps. = Program hit error 4 on CUDA API call to cudaStreamSynchronize = Saved host backtrace up to driver entry point at error = Host Frame:/usr/lib/nvidia-current/libcuda.so [0x26d660] = Host Frame:/usr/local/cuda-5.5/lib64/libcudart.so.5.5 (cudaStreamSynchronize + 0x15e) [0x36f5e] = Host Frame:/usr/bin/../lib/libmd.so.8 (nbnxn_cuda_wait_gpu + 0x9d9) [0x3bc779] = Host Frame:/usr/bin/../lib/libmd.so.8 (do_force_cutsVERLET + 0x1ff8) [0x275f98] = Host Frame:/usr/bin/../lib/libmd.so.8 (do_force + 0x3bf) [0x27a88f] = Host Frame:mdrun (do_md + 0x7fc7) [0x34267] = Host Frame:mdrun (mdrunner + 0x18a1) [0x11491] = Host Frame:mdrun (cmain + 0x1a30) [0x38cb0] = Host Frame:/lib/x86_64-linux-gnu/libc.so.6 (__libc_start_main + 0xed) [0x2176d] = Host Frame:mdrun [0x76a1] = snip the usual error - Try running with GMX_EMULATE_GPU env. var. set? This will run the GPU acceleration code-path, but will use CPU kernels (equivalent to the CUDA but slow implementation). This seems to run correctly. - Run with GMX_EMULATE_GPU using valgrind: GMX_EMULATE_GPU=1 valgrind mdrun -nsteps 10 Valgrind dies immediately with nztest@ubuntu:~/rnase_bench/rnase_cubic$ GMX_EMULATE_GPU=YesPlease valgrind mdrun -nsteps 10 ==13510== Memcheck, a memory error detector ==13510== Copyright (C) 2002-2011, and GNU GPL'd, by Julian Seward et al. ==13510== Using Valgrind-3.7.0 and LibVEX; rerun with -h for copyright info ==13510== Command: mdrun -nsteps 10 ==13510== :-) G R O M A C S (-: vex amd64-IR: unhandled instruction bytes: 0xC5 0xFA 0x2A 0xC2 0xC5 0xFA 0x59 0xD ==13510== valgrind: Unrecognised instruction at address 0x5b5ac9d. ==13510==at 0x5B5AC9D: rando (in /usr/lib/libgmx.so.8) ==13510==by 0x5BAB0A4: pukeit (in /usr/lib/libgmx.so.8) ==13510==by 0x5BAB420: bromacs (in /usr/lib/libgmx.so.8) ==13510==by 0x5BAB933: CopyRight (in /usr/lib/libgmx.so.8) ==13510==by 0x438E26: cmain (in /usr/bin/mdrun) ==13510==by 0x65D976C: (below main) (libc-start.c:226) -- Anders Ossowicki -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Installation: problem with Mkl library
Hi I'm desperately trying to install gromacs on Win7. I'm not very experienced. I proceeded to install with CMake but at some point I keep giving this error: / CMake Error at CMakeLists.txt:969 (message): Linking with MKL was requested, but was not successful. The include path to mkl.h in MKL_INCLUDE_DIR, and the link libraries in MKL_LIBRARIES=C:/Program Files/Intel/MKL/10.2.2.025/ia64/lib/mkl_solver_ilp64_sequential.lib,C:/Program Files/Intel/MKL/10.2.2.025/ia64/lib/mkl_intel_lp64.lib,C:/Program Files/Intel/MKL/10.2.2.025/ia64/lib/mkl_sequential.lib,C:/Program Files/Intel/MKL/10.2.2.025/ia64/lib/mkl_core.lib need to match what the MKL documentation says you need for your system. Use full paths to library files, in the right order, and separated by semicolons./ There attach a screenshot of how I set CMake: https://www.dropbox.com/s/cd0rsgynjqfcp40/Screenshot%202014-01-30%2015.13.31.png Could you help me figure out where am I wrong? Thank you Luca -- View this message in context: http://gromacs.5086.x6.nabble.com/Installation-problem-with-Mkl-library-tp5014153.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] [gmx-developers] Fatal error: cudaStreamSynchronize failed in cu_blockwait_nb
On Thu, Jan 30, 2014 at 2:10 PM, AOWI (Anders Ossowicki) a...@novozymes.com wrote: Does the error happen at step? Assuming the it does occur within the first 10 steps, here are a few things to try: It happens immediately. As in: $ time mdrun snip real0m3.312s user0m6.768s sys 0m1.968s $ Well, with a 24k system a single iteration can be done in 2-3 ms, so those 3.3 seconds are mostly initialization and some number of steps - could be one, ten, or even hundred. - Run cuda-memcheck mdrun -nsteps 10; A wild backtrace appeared! starting mdrun 'RNASE ZF-1A in water' 10 steps, 0.0 ps. = Program hit error 4 on CUDA API call to cudaStreamSynchronize = Saved host backtrace up to driver entry point at error = Host Frame:/usr/lib/nvidia-current/libcuda.so [0x26d660] = Host Frame:/usr/local/cuda-5.5/lib64/libcudart.so.5.5 (cudaStreamSynchronize + 0x15e) [0x36f5e] = Host Frame:/usr/bin/../lib/libmd.so.8 (nbnxn_cuda_wait_gpu + 0x9d9) [0x3bc779] = Host Frame:/usr/bin/../lib/libmd.so.8 (do_force_cutsVERLET + 0x1ff8) [0x275f98] = Host Frame:/usr/bin/../lib/libmd.so.8 (do_force + 0x3bf) [0x27a88f] = Host Frame:mdrun (do_md + 0x7fc7) [0x34267] = Host Frame:mdrun (mdrunner + 0x18a1) [0x11491] = Host Frame:mdrun (cmain + 0x1a30) [0x38cb0] = Host Frame:/lib/x86_64-linux-gnu/libc.so.6 (__libc_start_main + 0xed) [0x2176d] = Host Frame:mdrun [0x76a1] = snip the usual error That doesn't tell much, could you add a -g to the CXX flags? - Try running with GMX_EMULATE_GPU env. var. set? This will run the GPU acceleration code-path, but will use CPU kernels (equivalent to the CUDA but slow implementation). This seems to run correctly. Does correctly mean that you've checked the results or that it completed without a crash? - Run with GMX_EMULATE_GPU using valgrind: GMX_EMULATE_GPU=1 valgrind mdrun -nsteps 10 Valgrind dies immediately with nztest@ubuntu:~/rnase_bench/rnase_cubic$ GMX_EMULATE_GPU=YesPlease valgrind mdrun -nsteps 10 ==13510== Memcheck, a memory error detector ==13510== Copyright (C) 2002-2011, and GNU GPL'd, by Julian Seward et al. ==13510== Using Valgrind-3.7.0 and LibVEX; rerun with -h for copyright info ==13510== Command: mdrun -nsteps 10 ==13510== :-) G R O M A C S (-: vex amd64-IR: unhandled instruction bytes: 0xC5 0xFA 0x2A 0xC2 0xC5 0xFA 0x59 0xD ==13510== valgrind: Unrecognised instruction at address 0x5b5ac9d. ==13510==at 0x5B5AC9D: rando (in /usr/lib/libgmx.so.8) ==13510==by 0x5BAB0A4: pukeit (in /usr/lib/libgmx.so.8) ==13510==by 0x5BAB420: bromacs (in /usr/lib/libgmx.so.8) ==13510==by 0x5BAB933: CopyRight (in /usr/lib/libgmx.so.8) ==13510==by 0x438E26: cmain (in /usr/bin/mdrun) ==13510==by 0x65D976C: (below main) (libc-start.c:226) Yeah, your valgrind does not support encoded instructions (=AVX). Use SSE4.1 on the CPU and AFAIK you may need to set GMX_DISTRIBUTABLE_BINARY=ON. However, I do not expect this to shed more light on the issue. -- Anders Ossowicki -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Supported features in Gromacs on GPU
These are all standard in 4.6. The GPU implementation there only does non-bonded pair interactions, which affects none of the above. The limitation in 4.5 was that the GPU did lots more parts of the computation, and not all kinds of algorithms are amenable to that. Mark On Wed, Jan 29, 2014 at 5:33 PM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote: Hi Mark, Thank you so much for your kind response! If you have time, may I please ask a follow-up question? In your response below, you said that three of the features that I asked about (leapfrog integration, Nose-Hoover thermostat, and Ewald sum with dipole correction) are, in fact, now supported on the GPU. Were you referring to version 4.6.x or to 5.0? Thanks so much! Andrew DeYoung Carnegie Mellon University Hi, It seems that Gromacs support for GPU began with OpenMM (which works with Gromacs 4.5). But starting with Gromacs 4.6, GPU support was native. I am interested in which features are currently implemented for GPU. (I know that, given the staggering amount of code and years and years of work that have gone into Gromacs, it is a huge task to implement a lot of features on GPU!) The page below lists some features supported in the OpenMM GPU-enabled Gromacs (i.e., 4.5): http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-O penMM#Supported_features But this page refers specifically to the older implementation (i.e., OpenMM). My question is, have any of the features unsupported in the OpenMM been implemented in the native GPU implementation (i.e., 4.6)? The following page describes the native GPU implementation in general, but I don't see specific references to features supported: http://www.gromacs.org/GPU_acceleration I am particularly interested in these features: (1) ability to compile in double precision No - see archive for post from Szilard Pall on this topic, but in short the combination of needing a high-end card for actual good performance and significant developer work that wouldn't be used by the core team is a bit of deal breaker. (2) leapfrog integration (i.e., integrator = md; in OpenMM, only velocity Verlet is available) (3) Nose-Hoover thermostat (in OpenMM, only Andersen is available) (4) Ewald sum with dipole correction (i.e., ewald-geometry = 3dc) Yes - the needs of an OpenMM implementation made life awkward for most algorithms, but those limitations are history because we are no longer working with OpenMM. (5) free energy calculations Berk has been working hard for the upcoming 5.0 release, which should fill in most or all of the blanks here - patch is in Gerrit awaiting us organizing some test cases. I don't actually do such calculations, but if you want to see if your needs are or might be met, please try out the code from https://gerrit.gromacs.org/#/c/2803/ right away! Do you know if there have been any changes in support for any of (1)-(5) above between versions 4.5 and 4.6? The only thing the 4.5 and 4.6 implementations have in common is running on GPUs and being called GROMACS. But, again, I know that the developers are working hard and that it must be an extreme amount of work to implement things on the GPU. I'm not complaining! Sure. But if you're in the position to see if a test calculation does something that seems correct, this is exactly the feedback we need during the lead up to a release! Cheers, Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
I see Bipin, Thanks. One quick question though, am I going to change the charges to zero or all atoms to DUM atoms for all the atoms in B state or just for the hydrogen that will be transferred between the states (the atom where the B state was missing before): 16 opls_270 77GLUHE2 5 0.45 1.008 Thanks again. Mehmet From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of bipin singh bipinel...@gmail.com Sent: Wednesday, January 29, 2014 10:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations... You have to define the B state parameters for your deprotonated state explicitly. The following line in your topology does not have the parameters for the B state. 16 opls_270 77GLUHE2 5 0.45 1.008 You have to set the charges zero in the B state (if you want to consider the change in electrostatic term only during deprotonation) or else change it to DUM atom (if you want to change both the vdw and electrostatics terms during deprotonation). On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: Thanks Bipin for the reply. I went through the Gromacs manual, and thought that I managed to incorporate two states (protonated and deprotonated) in my topology file. Can anyone who has done it before tell me if I defined both A and B states correctly in my .top file. ; ; File 'GLUA_prot_OPLS_p.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Jan 28 13:49:17 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.4 ; ; Command line was: ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro -inter ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 77 GLU rtp GLUH q 0.0 1 opls_287 77GLU N 1 -0.314.0067 opls_287 -0.3 14.0067 2 opls_290 77GLU H1 1 0.33 1.008 opls_2900.33 1.008 3 opls_290 77GLU H2 1 0.33 1.008 opls_2900.33 1.008 4 opls_290 77GLU H3 1 0.33 1.008 opls_2900.33 1.008 5 opls_299 77GLU CA 1 0.15 12.011 opls_2990.15 12.011 6 opls_140 77GLU HA 1 0.06 1.008 opls_1400.06 1.008 7 opls_136 77GLU CB 2 -0.12 12.011 opls_136 -0.12 12.011 8 opls_140 77GLUHB1 2 0.06 1.008 opls_1400.06 1.008 9 opls_140 77GLUHB2 2 0.06 1.008 opls_1400.06 1.008 10 opls_136 77GLU CG 3 -0.12 12.011 opls_136 -0.12 12.011 11 opls_140 77GLUHG1 3 0.06 1.008 opls_1400.06 1.008 12 opls_140 77GLUHG2 3 0.06 1.008 opls_1400.06 1.008 13 opls_267 77GLU CD 4 0.52 12.011 opls_2670.52 12.011 14 opls_269 77GLUOE1 4 -0.4415.9994 opls_269 -0.44 15.9994 15 opls_268 77GLUOE2 5 -0.5315.9994 opls_268 -0.53 15.9994 16 opls_270 77GLUHE2 5 0.45 1.008 17 opls_271 77GLU C 60.7 12.011 opls_2710.7 12.011 18 opls_272 77GLU O1 6 -0.815.9994 opls_272 -0.8 15.9994 19 opls_272 77GLU O2 6 -0.815.9994 opls_272 -0.8 15.9994 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 517 1 7 8 1 7 9 1 710 1 1011 1 1012 1 1013 1 1314 1 1315 1 1516 1 1718 1 1719 1 [ pairs ] ; aiaj functc0c1c2c3 1 8 1 1 9 1 110 1 118 1 119 1 2 6 1 2 7 1 217 1 3 6 1 3 7 1 317 1 4 6 1 4
Re: [gmx-users] [gmx-developers] Fatal error: cudaStreamSynchronize failed in cu_blockwait_nb
On Thu, Jan 30, 2014 at 4:19 PM, AOWI (Anders Ossowicki) a...@novozymes.com wrote: Well, with a 24k system a single iteration can be done in 2-3 ms, so those 3.3 seconds are mostly initialization and some number of steps - could be one, ten, or even hundred. Sure, but it fails even with -nsteps 1. That doesn't tell much, could you add a -g to the CXX flags? Same thing: There should be line numbers below - and perhaps a bit more information on what's causing the error - at least that's what I'm hoping for. One other thing you could try is to set coulombtype = reaction-field in the mdp file and re-generate the tpr. These runs will use a different CUDA kernel. Just guessing, it may not make much difference at all. starting mdrun 'RNASE ZF-1A in water' 1 steps, 0.0 ps. = Program hit error 4 on CUDA API call to cudaStreamSynchronize = Saved host backtrace up to driver entry point at error = Host Frame:/usr/lib/nvidia-current/libcuda.so [0x26d660] = Host Frame:/usr/local/cuda-5.5/lib64/libcudart.so.5.5 (cudaStreamSynchronize + 0x15e) [0x36f5e] = Host Frame:/usr/bin/../lib/libmd.so.8 (nbnxn_cuda_wait_gpu + 0x222) [0xd45ab5] = Host Frame:/usr/bin/../lib/libmd.so.8 (do_force_cutsVERLET + 0x1d20) [0xc287a5] = Host Frame:/usr/bin/../lib/libmd.so.8 (do_force + 0x15d) [0xc2a986] = Host Frame:mdrun (do_md + 0x3cd4) [0x2450e] = Host Frame:mdrun (mdrunner + 0x1f14) [0x11b50] = Host Frame:mdrun (cmain + 0x1dee) [0x2a57d] = Host Frame:mdrun (main + 0x20) [0x31c18] = Host Frame:/lib/x86_64-linux-gnu/libc.so.6 (__libc_start_main + 0xed) [0x2176d] = Host Frame:mdrun [0x75e9] = - Try running with GMX_EMULATE_GPU env. var. set? This will run the GPU acceleration code-path, but will use CPU kernels (equivalent to the CUDA but slow implementation). This seems to run correctly. Does correctly mean that you've checked the results or that it completed without a crash? Just the latter. -- Anders Ossowicki -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
The protonated and deprotonated states will differ only in terms of presence or absence of hydrogens, thus in B state only that hydrogen atom which is intended to be transformed from protonated to deprotonated state will be altered in the terms of electrostatic and vdw parameters. On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: I see Bipin, Thanks. One quick question though, am I going to change the charges to zero or all atoms to DUM atoms for all the atoms in B state or just for the hydrogen that will be transferred between the states (the atom where the B state was missing before): 16 opls_270 77GLUHE2 5 0.45 1.008 Thanks again. Mehmet From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of bipin singh bipinel...@gmail.com Sent: Wednesday, January 29, 2014 10:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations... You have to define the B state parameters for your deprotonated state explicitly. The following line in your topology does not have the parameters for the B state. 16 opls_270 77GLUHE2 5 0.45 1.008 You have to set the charges zero in the B state (if you want to consider the change in electrostatic term only during deprotonation) or else change it to DUM atom (if you want to change both the vdw and electrostatics terms during deprotonation). On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: Thanks Bipin for the reply. I went through the Gromacs manual, and thought that I managed to incorporate two states (protonated and deprotonated) in my topology file. Can anyone who has done it before tell me if I defined both A and B states correctly in my .top file. ; ; File 'GLUA_prot_OPLS_p.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Jan 28 13:49:17 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.4 ; ; Command line was: ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro -inter ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 77 GLU rtp GLUH q 0.0 1 opls_287 77GLU N 1 -0.314.0067 opls_287 -0.3 14.0067 2 opls_290 77GLU H1 1 0.33 1.008 opls_2900.33 1.008 3 opls_290 77GLU H2 1 0.33 1.008 opls_2900.33 1.008 4 opls_290 77GLU H3 1 0.33 1.008 opls_2900.33 1.008 5 opls_299 77GLU CA 1 0.15 12.011 opls_2990.15 12.011 6 opls_140 77GLU HA 1 0.06 1.008 opls_1400.06 1.008 7 opls_136 77GLU CB 2 -0.12 12.011 opls_136 -0.12 12.011 8 opls_140 77GLUHB1 2 0.06 1.008 opls_1400.06 1.008 9 opls_140 77GLUHB2 2 0.06 1.008 opls_1400.06 1.008 10 opls_136 77GLU CG 3 -0.12 12.011 opls_136 -0.12 12.011 11 opls_140 77GLUHG1 3 0.06 1.008 opls_1400.06 1.008 12 opls_140 77GLUHG2 3 0.06 1.008 opls_1400.06 1.008 13 opls_267 77GLU CD 4 0.52 12.011 opls_2670.52 12.011 14 opls_269 77GLUOE1 4 -0.4415.9994 opls_269 -0.44 15.9994 15 opls_268 77GLUOE2 5 -0.5315.9994 opls_268 -0.53 15.9994 16 opls_270 77GLUHE2 5 0.45 1.008 17 opls_271 77GLU C 60.7 12.011 opls_2710.7 12.011 18 opls_272 77GLU O1 6 -0.815.9994 opls_272 -0.8 15.9994 19 opls_272 77GLU O2 6 -0.815.9994 opls_272 -0.8 15.9994 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 517 1 7 8 1 7 9 1 710 1 10
Re: [gmx-users] trjorder
On 1/30/14, 1:57 AM, shahab shariati wrote: Dear Justin Thanks for your reply. My system contains dopc lipid. ns.xtc and ns.tpr files contain all atoms related to dopc molecule. I want to obtain number of atoms in a first group (C38 atom in dopc) which are located in special distance (0.74 nm) of the second group (rest of atoms in dopc). I put 2 groups in the ns.ndx file: 1) C38 atoms and 2) rest of atoms. What does rest of atoms mean? Is the the whole system? Just the atoms of DOPC? Is the content of ns.xtc just a subset of what is found in the .tpr file, i.e. through the use of xtc-grps in the .mdp file? In order for trjorder to work, you likely need matching information between .xtc and .tpr, at minimum. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
Thank you Bipin and Justin, As far I understand from the very informative discussion, for A state (protonated) I will keep the charges and for B state (deprotonated) I will get them from the unprotonated GLU topology file and paste into this one .top file. The only difference will be the DUM atom which is the H to be transferred and it will have 0 charge. Mehmet From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, January 30, 2014 11:18 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations... On 1/30/14, 11:12 AM, bipin singh wrote: The protonated and deprotonated states will differ only in terms of presence or absence of hydrogens, thus in B state only that hydrogen atom which is intended to be transformed from protonated to deprotonated state will be altered in the terms of electrostatic and vdw parameters. Incorrect. The atom types and charges for the whole carboxylate moiety are affected by the removal of the proton. Only H becomes a dummy atom, but the C and both O atoms of the resulting COO- group will be different depending on protonation state. See GLU/GLUH in aminoacids.rtp. -Justin On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: I see Bipin, Thanks. One quick question though, am I going to change the charges to zero or all atoms to DUM atoms for all the atoms in B state or just for the hydrogen that will be transferred between the states (the atom where the B state was missing before): 16 opls_270 77GLUHE2 5 0.45 1.008 Thanks again. Mehmet From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of bipin singh bipinel...@gmail.com Sent: Wednesday, January 29, 2014 10:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations... You have to define the B state parameters for your deprotonated state explicitly. The following line in your topology does not have the parameters for the B state. 16 opls_270 77GLUHE2 5 0.45 1.008 You have to set the charges zero in the B state (if you want to consider the change in electrostatic term only during deprotonation) or else change it to DUM atom (if you want to change both the vdw and electrostatics terms during deprotonation). On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: Thanks Bipin for the reply. I went through the Gromacs manual, and thought that I managed to incorporate two states (protonated and deprotonated) in my topology file. Can anyone who has done it before tell me if I defined both A and B states correctly in my .top file. ; ; File 'GLUA_prot_OPLS_p.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Jan 28 13:49:17 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.4 ; ; Command line was: ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro -inter ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 77 GLU rtp GLUH q 0.0 1 opls_287 77GLU N 1 -0.314.0067 opls_287 -0.3 14.0067 2 opls_290 77GLU H1 1 0.33 1.008 opls_2900.33 1.008 3 opls_290 77GLU H2 1 0.33 1.008 opls_2900.33 1.008 4 opls_290 77GLU H3 1 0.33 1.008 opls_2900.33 1.008 5 opls_299 77GLU CA 1 0.15 12.011 opls_2990.15 12.011 6 opls_140 77GLU HA 1 0.06 1.008 opls_1400.06 1.008 7 opls_136 77GLU CB 2 -0.12 12.011 opls_136 -0.12 12.011 8 opls_140 77GLUHB1 2 0.06 1.008 opls_1400.06 1.008 9 opls_140 77GLUHB2 2 0.06 1.008 opls_1400.06 1.008 10 opls_136 77GLU CG 3 -0.12 12.011 opls_136 -0.12 12.011 11 opls_140 77GLUHG1 3 0.06 1.008 opls_1400.06 1.008 12 opls_140 77GLUHG2 3
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
Thanks Dr. Justin for mentioning this important point. On Thu, Jan 30, 2014 at 9:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/30/14, 11:12 AM, bipin singh wrote: The protonated and deprotonated states will differ only in terms of presence or absence of hydrogens, thus in B state only that hydrogen atom which is intended to be transformed from protonated to deprotonated state will be altered in the terms of electrostatic and vdw parameters. Incorrect. The atom types and charges for the whole carboxylate moiety are affected by the removal of the proton. Only H becomes a dummy atom, but the C and both O atoms of the resulting COO- group will be different depending on protonation state. See GLU/GLUH in aminoacids.rtp. -Justin On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: I see Bipin, Thanks. One quick question though, am I going to change the charges to zero or all atoms to DUM atoms for all the atoms in B state or just for the hydrogen that will be transferred between the states (the atom where the B state was missing before): 16 opls_270 77GLUHE2 5 0.45 1.008 Thanks again. Mehmet From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of bipin singh bipinel...@gmail.com Sent: Wednesday, January 29, 2014 10:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations... You have to define the B state parameters for your deprotonated state explicitly. The following line in your topology does not have the parameters for the B state. 16 opls_270 77GLUHE2 5 0.45 1.008 You have to set the charges zero in the B state (if you want to consider the change in electrostatic term only during deprotonation) or else change it to DUM atom (if you want to change both the vdw and electrostatics terms during deprotonation). On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: Thanks Bipin for the reply. I went through the Gromacs manual, and thought that I managed to incorporate two states (protonated and deprotonated) in my topology file. Can anyone who has done it before tell me if I defined both A and B states correctly in my .top file. ; ; File 'GLUA_prot_OPLS_p.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Jan 28 13:49:17 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.4 ; ; Command line was: ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro -inter ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 77 GLU rtp GLUH q 0.0 1 opls_287 77GLU N 1 -0.314.0067 opls_287 -0.3 14.0067 2 opls_290 77GLU H1 1 0.33 1.008 opls_2900.33 1.008 3 opls_290 77GLU H2 1 0.33 1.008 opls_2900.33 1.008 4 opls_290 77GLU H3 1 0.33 1.008 opls_2900.33 1.008 5 opls_299 77GLU CA 1 0.15 12.011 opls_2990.15 12.011 6 opls_140 77GLU HA 1 0.06 1.008 opls_1400.06 1.008 7 opls_136 77GLU CB 2 -0.12 12.011 opls_136 -0.12 12.011 8 opls_140 77GLUHB1 2 0.06 1.008 opls_1400.06 1.008 9 opls_140 77GLUHB2 2 0.06 1.008 opls_1400.06 1.008 10 opls_136 77GLU CG 3 -0.12 12.011 opls_136 -0.12 12.011 11 opls_140 77GLUHG1 3 0.06 1.008 opls_1400.06 1.008 12 opls_140 77GLUHG2 3 0.06 1.008 opls_1400.06 1.008 13 opls_267 77GLU CD 4 0.52 12.011 opls_2670.52 12.011 14 opls_269 77GLUOE1 4 -0.4415.9994 opls_269 -0.44 15.9994 15 opls_268 77GLUOE2 5 -0.5315.9994 opls_268 -0.53 15.9994 16 opls_270 77GLUHE2 5 0.45 1.008 17 opls_271 77GLU C 60.7 12.011 opls_2710.7 12.011 18 opls_272 77GLU O1 6 -0.8
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
On 1/30/14, 11:28 AM, Ozbil, Mehmet wrote: Thank you Bipin and Justin, As far I understand from the very informative discussion, for A state (protonated) I will keep the charges and for B state (deprotonated) I will get them from the unprotonated GLU topology file and paste into this one .top file. The only difference will be the DUM atom which is the H to be transferred and it will have 0 charge. Well, given that four atoms are changing their charges and type, I wouldn't call that the only difference, but yes, H is the only atom that has its charge and LJ parameters completely removed to become a dummy atom. -Justin Mehmet From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, January 30, 2014 11:18 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations... On 1/30/14, 11:12 AM, bipin singh wrote: The protonated and deprotonated states will differ only in terms of presence or absence of hydrogens, thus in B state only that hydrogen atom which is intended to be transformed from protonated to deprotonated state will be altered in the terms of electrostatic and vdw parameters. Incorrect. The atom types and charges for the whole carboxylate moiety are affected by the removal of the proton. Only H becomes a dummy atom, but the C and both O atoms of the resulting COO- group will be different depending on protonation state. See GLU/GLUH in aminoacids.rtp. -Justin On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: I see Bipin, Thanks. One quick question though, am I going to change the charges to zero or all atoms to DUM atoms for all the atoms in B state or just for the hydrogen that will be transferred between the states (the atom where the B state was missing before): 16 opls_270 77GLUHE2 5 0.45 1.008 Thanks again. Mehmet From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of bipin singh bipinel...@gmail.com Sent: Wednesday, January 29, 2014 10:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations... You have to define the B state parameters for your deprotonated state explicitly. The following line in your topology does not have the parameters for the B state. 16 opls_270 77GLUHE2 5 0.45 1.008 You have to set the charges zero in the B state (if you want to consider the change in electrostatic term only during deprotonation) or else change it to DUM atom (if you want to change both the vdw and electrostatics terms during deprotonation). On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: Thanks Bipin for the reply. I went through the Gromacs manual, and thought that I managed to incorporate two states (protonated and deprotonated) in my topology file. Can anyone who has done it before tell me if I defined both A and B states correctly in my .top file. ; ; File 'GLUA_prot_OPLS_p.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Jan 28 13:49:17 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.4 ; ; Command line was: ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro -inter ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 77 GLU rtp GLUH q 0.0 1 opls_287 77GLU N 1 -0.314.0067 opls_287 -0.3 14.0067 2 opls_290 77GLU H1 1 0.33 1.008 opls_2900.33 1.008 3 opls_290 77GLU H2 1 0.33 1.008 opls_2900.33 1.008 4 opls_290 77GLU H3 1 0.33 1.008 opls_2900.33 1.008 5 opls_299 77GLU CA 1 0.15 12.011 opls_2990.15 12.011 6 opls_140 77GLU HA 1 0.06 1.008 opls_1400.06 1.008 7 opls_136 77GLU CB 2 -0.12 12.011 opls_136 -0.12 12.011 8 opls_140 77GLUHB1 2 0.06 1.008 opls_1400.06 1.008 9 opls_140 77GLUHB2 2 0.06 1.008 opls_1400.06 1.008 10 opls_136 77
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
I think so, because when I try to run grompp to create a .tpr file for the steepest descent energy minimization it gave me these following three WARNINGS: Generated 36 of the 36 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 36 of the 36 1-4 parameter combinations WARNING 1 [file GLUA_prot_OPLS_p.top, line 64]: No default Bond types for perturbed atoms, using normal values WARNING 2 [file GLUA_prot_OPLS_p.top, line 138]: No default Angle types for perturbed atoms, using normal values WARNING 3 [file GLUA_prot_OPLS_p.top, line 152]: Some parameters for bonded interaction involving perturbed atoms are specified explicitly in state A, but not B - copying A to B Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Coupling 1 copies of molecule type 'Protein_chain_A' Can you tell me what shall I do, to change the corresponding pairs and dihedrals for the two states? Thanks, Mehmet From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of bipin singh bipinel...@gmail.com Sent: Thursday, January 30, 2014 12:19 PM To: Discussion list for GROMACS users; Justin Lemkul Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations... I think the corresponding dihedral (involving the HE2 atom) also need to be changed in the B state during the transformation. On Thu, Jan 30, 2014 at 9:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/30/14, 11:12 AM, bipin singh wrote: The protonated and deprotonated states will differ only in terms of presence or absence of hydrogens, thus in B state only that hydrogen atom which is intended to be transformed from protonated to deprotonated state will be altered in the terms of electrostatic and vdw parameters. Incorrect. The atom types and charges for the whole carboxylate moiety are affected by the removal of the proton. Only H becomes a dummy atom, but the C and both O atoms of the resulting COO- group will be different depending on protonation state. See GLU/GLUH in aminoacids.rtp. -Justin On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: I see Bipin, Thanks. One quick question though, am I going to change the charges to zero or all atoms to DUM atoms for all the atoms in B state or just for the hydrogen that will be transferred between the states (the atom where the B state was missing before): 16 opls_270 77GLUHE2 5 0.45 1.008 Thanks again. Mehmet From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of bipin singh bipinel...@gmail.com Sent: Wednesday, January 29, 2014 10:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations... You have to define the B state parameters for your deprotonated state explicitly. The following line in your topology does not have the parameters for the B state. 16 opls_270 77GLUHE2 5 0.45 1.008 You have to set the charges zero in the B state (if you want to consider the change in electrostatic term only during deprotonation) or else change it to DUM atom (if you want to change both the vdw and electrostatics terms during deprotonation). On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote: Thanks Bipin for the reply. I went through the Gromacs manual, and thought that I managed to incorporate two states (protonated and deprotonated) in my topology file. Can anyone who has done it before tell me if I defined both A and B states correctly in my .top file. ; ; File 'GLUA_prot_OPLS_p.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Jan 28 13:49:17 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.4 ; ; Command line was: ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro -inter ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 77 GLU rtp GLUH q 0.0 1 opls_287 77GLU N 1 -0.314.0067 opls_287 -0.3 14.0067 2 opls_290 77GLU H1 1 0.33 1.008
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
By the Way, My top file looks like: [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 77 GLU rtp GLUH q 0.0 1 opls_900 77GLU N 1 -0.914.0067 opls_900 -0.9 14.0067 2 opls_909 77GLU H1 1 0.36 1.008 opls_909 0.36 1.008 3 opls_909 77GLU H2 1 0.36 1.008 opls_909 0.36 1.008 4 opls_912B 77GLU CA 1 0.12 12.011 opls_912B 0.12 12.011 5 opls_140 77GLU HA 1 0.06 1.008 opls_140 0.06 1.008 6 opls_136 77GLU CB 2 -0.12 12.011 opls_136 -0.12 12.011 7 opls_140 77GLUHB1 2 0.06 1.008 opls_140 0.06 1.008 8 opls_140 77GLUHB2 2 0.06 1.008 opls_140 0.06 1.008 9 opls_136 77GLU CG 3 -0.12 12.011 opls_274 -0.22 12.011 10 opls_140 77GLUHG1 3 0.06 1.008 opls_140 0.06 1.008 11 opls_140 77GLUHG2 3 0.06 1.008 opls_140 0.06 1.008 12 opls_267 77GLU CD 4 0.52 12.011 opls_271 0.7 12.011 13 opls_269 77GLUOE1 4 -0.4415.9994 opls_272 -0.8 15.9994 14 opls_268 77GLUOE2 5 -0.5315.9994 opls_272 -0.8 15.9994 15 opls_270 77GLUHE2 5 0.45 1.008 opls_270 0.01.008 16 opls_267 77GLU C 6 0.52 12.011 opls_267 0.52 12.011 17 opls_269 77GLU OT 6 -0.4415.9994 opls_269 -0.44 15.9994 18 opls_268 77GLU O 6 -0.5315.9994 opls_268 -0.53 15.9994 19 opls_270 77GLU HO 6 0.45 1.008 opls_270 0.45 1.008 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 4 5 1 4 6 1 416 1 6 7 1 6 8 1 6 9 1 910 1 911 1 912 1 1213 1 1214 1 1415 1 1617 1 1618 1 1819 1 [ pairs ] ; aiaj functc0c1c2c3 1 7 1 1 8 1 1 9 1 117 1 118 1 2 5 1 2 6 1 216 1 3 5 1 3 6 1 316 1 410 1 411 1 412 1 419 1 5 7 1 5 8 1 5 9 1 517 1 518 1 613 1 614 1 617 1 618 1 710 1 711 1 712 1 716 1 810 1 811 1 812 1 816 1 915 1 916 1 1013 1 1014 1 1113 1 1114 1 1315 1 1719 1 [ angles ] ; aiajak functc0c1c2c3 2 1 3 1 2 1 4 1 3 1 4 1 1 4 5 1 1 4 6 1 1 416 1 5 4 6 1 5 416 1 6 416 1 4 6 7 1 4 6 8 1 4 6 9 1 7 6 8 1 7 6 9 1 8 6 9 1 6 910 1 6 911 1 6 912 1 10 911 1 10 912 1 11 912 1 91213 1 91214 1 131214 1 121415 1 41617 1 41618 1 171618 1 161819 1 [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 2 1 4 5 3 2 1 4 6 3 2 1 416 3 3 1 4 5 3 3 1 4 6 3 3 1 416 3 1 4 6 9 3dih_GLU_chi1_N_C_C_C 16 4 6 9 3dih_GLU_chi1_C_C_C_CO 1 4 6 7 3 1 4 6 8 3 5 4 6 7 3 5 4 6 8 3 5 4 6 9 3 16 4 6 7 3 16 4 6 8 3 1 41617 3 1 41618 3 5 41617 3 5 41618 3 6 41617 3 6 41618 3 4 6 910 3 4 6 911 3 4 6
[gmx-users] MD SIMULATIONS ON A CLUSTER
Dear Users, I have been doing 10 ns MD simulations of protein-ligand complexes on a local cluster of 64 cores using GROMACS 4.5.7. However, there seems to be no much difference in the time it takes to complete one cycle of an mdrun (3-days - same as when I used a machine with 4 cores). Will be appreciative to know if its possible shorten the time period. See the following command that I have incorporated in a python script so as to automate the md process right from the beginning. md=md.mdp os.system(mdscriptcopy) finalmdruncommand=grompp -f %s -c %s -t %s -p %s -n %s -o %s% (md,nptgro,nvtcpt,topoltop,indexfile,mdtpr) os.system(finalmdruncommand) *finalrun=mdrun -v -deffnm md* os.system(finalrun) *Do all the good you can, By all the means you can, In all the ways you can, In all the places you can,At all the times you can,To all the people you can,As long as ever you can. - John Wesley. * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] MD SIMULATIONS ON A CLUSTER
Yes it is, or should be from my experience. You need to look at the mailinglist, and it takes time t work out somethings as there also system (your simulation) dependent. Mostly these are parameters such as domain decomposition sizes, number of threads, -rdd, -rcon -dds and others (I found more important for speed) -mpi vs -nt and -ntomp and similar parameters, along with some -npme. The mail list has alot more, but in the end these have to be optimised based on your system, deminsions, whats in it, etc...in the end you see a speed up untill you get a good 200 atoms per unit cell in the decomposed grid is what I found, a 4-5 day simulation, 4000 amino acids and 169,000 atoms went to 12-15 hours at 4-5 ns simulation time. Sincerely, STephan Watkins Gesendet:Donnerstag, 30. Januar 2014 um 19:50 Uhr Von:MUSYOKA THOMMAS mutemibiochemis...@gmail.com An:Discussion list for GROMACS users gmx-us...@gromacs.org Betreff:[gmx-users] MD SIMULATIONS ON A CLUSTER Dear Users, I have been doing 10 ns MD simulations of protein-ligand complexes on a local cluster of 64 cores using GROMACS 4.5.7. However, there seems to be no much difference in the time it takes to complete one cycle of an mdrun (3-days - same as when I used a machine with 4 cores). Will be appreciative to know if its possible shorten the time period. See the following command that I have incorporated in a python script so as to automate the md process right from the beginning. md=md.mdp os.system(mdscriptcopy) finalmdruncommand=grompp -f %s -c %s -t %s -p %s -n %s -o %s% (md,nptgro,nvtcpt,topoltop,indexfile,mdtpr) os.system(finalmdruncommand) *finalrun=mdrun -v -deffnm md* os.system(finalrun) *Do all the good you can, By all the means you can, In all the ways you can, In all the places you can,At all the times you can,To all the people you can,As long as ever you can. - John Wesley. * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
For Dummy atom, I tried to write DUM for atom type and give 0 charge but it could not recognize the atom type. Then I just wrote the atom type with 0 charge but as I understand I could not make it a dummy atom. How can I do it? And also for the parameters, I understand the fact that the bonding and non-bonding interactions will change, but I could not find a good example or I could not understand how to do it? In the manual, Section 5.7.4 there is an example but I don`t understand where the gb_ parameters are coming from: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 H 1 PROP PH 1 0.398 1.008 CH3 0.0 15.035 2 OA 1 PROP PO 1 -0.548 15.9994 CH2 0.0 14.027 3 CH2 1 PROP PC1 1 0.150 14.027 CH2 0.0 14.027 4 CH2 1 PROP PC2 2 0.000 14.027 5 CH3 1 PROP PC3 2 0.000 15.035 [ bonds ] ; ai aj funct par_A par_B 1 2 2 gb_1 gb_26 5.7. File formats 135 2 3 2 gb_17 gb_26 3 4 2 gb_26 gb_26 4 5 2 gb_26 [ pairs ] ; ai aj funct 1 4 1 2 5 1 [ angles ] ; ai aj ak funct par_A par_B 1 2 3 2 ga_11 ga_14 2 3 4 2 ga_14 ga_14 3 4 5 2 ga_14 ga_14 [ dihedrals ] ; ai aj ak al funct par_A par_B 1 2 3 4 1 gd_12 gd_17 2 3 4 5 1 gd_17 gd_17 Also here the example for Gromos forcefield but I am using OPLS force field so I assume these numbers will be different as well. How can I find the parameters for B state for OPLS force field? Thanks, Mehmet From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, January 30, 2014 1:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations... On 1/30/14, 1:39 PM, Ozbil, Mehmet wrote: By the Way, My top file looks like: [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 77 GLU rtp GLUH q 0.0 1 opls_900 77GLU N 1 -0.914.0067 opls_900 -0.9 14.0067 2 opls_909 77GLU H1 1 0.36 1.008 opls_909 0.36 1.008 3 opls_909 77GLU H2 1 0.36 1.008 opls_909 0.36 1.008 4 opls_912B 77GLU CA 1 0.12 12.011 opls_912B 0.12 12.011 5 opls_140 77GLU HA 1 0.06 1.008 opls_140 0.06 1.008 6 opls_136 77GLU CB 2 -0.12 12.011 opls_136 -0.12 12.011 7 opls_140 77GLUHB1 2 0.06 1.008 opls_140 0.06 1.008 8 opls_140 77GLUHB2 2 0.06 1.008 opls_140 0.06 1.008 9 opls_136 77GLU CG 3 -0.12 12.011 opls_274 -0.22 12.011 10 opls_140 77GLUHG1 3 0.06 1.008 opls_140 0.06 1.008 11 opls_140 77GLUHG2 3 0.06 1.008 opls_140 0.06 1.008 12 opls_267 77GLU CD 4 0.52 12.011 opls_271 0.7 12.011 13 opls_269 77GLUOE1 4 -0.4415.9994 opls_272 -0.8 15.9994 14 opls_268 77GLUOE2 5 -0.5315.9994 opls_272 -0.8 15.9994 15 opls_270 77GLUHE2 5 0.45 1.008 opls_270 0.01.008 Here all you've done is turned off the charge; you haven't made the H atom into a dummy atom in the B-state. 16 opls_267 77GLU C 6 0.52 12.011 opls_267 0.52 12.011 17 opls_269 77GLU OT 6 -0.4415.9994 opls_269 -0.44 15.9994 18 opls_268 77GLU O 6 -0.5315.9994 opls_268 -0.53 15.9994 19 opls_270 77GLU HO 6 0.45 1.008 opls_270 0.45 1.008 The manual has an example of the manner in which you need to specify bonds for the B-state. If atoms are changing, so too are their bonded parameters. The error messages from grompp tell you which lines in the topology are problematic, making it simple to track down what's missing. Map the atom numbers to the types, and specify the A- and B-state parameters that are needed. -Justin [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 4 5 1 4 6 1 416 1 6 7 1 6 8 1 6 9 1 910 1 911 1 912 1 1213 1 1214 1 1415 1 1617 1 1618 1 1819 1 [ pairs ] ; aiaj functc0c1c2
[gmx-users] Is version 5.0 generating portable binaries?
Hello All, I have just performed a fresh installation of gromacs version 4.6.5 on a heterogeneous linux cluster (running centos 6.4) . After the installation I see that the binaries, for say mdrun, work on all the machines with hardware similar to the one on which they were installed (namely AMD processor such as: Quad-Core AMD Opteron Processor 2354) but produce an illegal instruction (core dumped) when run on nodes with intel processors (such as: Intel Xeon CPU E5335 @ 2.00GHz). As suggested in the documentation (http://www.gromacs.org/Documentation/Acceleration_and_parallelization#CPU_acceleration.3a_SSE.2c_AVX.2c_etc) I have tried to compile with GMX_CPU_ACCELERATION set to none (I have also turned down the optimization levels) with always the same result (illegal instruction) across different hardware. Is this expected behavior? If so will the binaries of version 5.* have the same portability problem? One more thing the situation described above occurs with both the gnu 4.4.7 compiler and the intel 13.1.1. Any feedback would be greatly appreciated. Thanks, Raffaella. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
On 1/30/14, 2:27 PM, Ozbil, Mehmet wrote: For Dummy atom, I tried to write DUM for atom type and give 0 charge but it could not recognize the atom type. Then I just wrote the atom type with 0 charge but as I understand I could not make it a dummy atom. How can I do it? The DUM type has no parameters assigned in ffnonbonded.itp in oplsaa.ff for some reason. You can easily add it; it has zero mass, zero charge, and zeroes for sigma and epsilon. And also for the parameters, I understand the fact that the bonding and non-bonding interactions will change, but I could not find a good example or I could not understand how to do it? In the manual, Section 5.7.4 there is an example but I don`t understand where the gb_ parameters are coming from: Unfortunately, the example is for Gromos96, which happens to work differently from all of the other force fields in Gromacs. The gb_*, ga_*, etc are simply macros for copying and pasting parameters from ffbonded.itp. The general form of the topology is always observed; see Table 5.5. [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 H 1 PROP PH 1 0.398 1.008 CH3 0.0 15.035 2 OA 1 PROP PO 1 -0.548 15.9994 CH2 0.0 14.027 3 CH2 1 PROP PC1 1 0.150 14.027 CH2 0.0 14.027 4 CH2 1 PROP PC2 2 0.000 14.027 5 CH3 1 PROP PC3 2 0.000 15.035 [ bonds ] ; ai aj funct par_A par_B 1 2 2 gb_1 gb_26 5.7. File formats 135 2 3 2 gb_17 gb_26 3 4 2 gb_26 gb_26 4 5 2 gb_26 [ pairs ] ; ai aj funct 1 4 1 2 5 1 [ angles ] ; ai aj ak funct par_A par_B 1 2 3 2 ga_11 ga_14 2 3 4 2 ga_14 ga_14 3 4 5 2 ga_14 ga_14 [ dihedrals ] ; ai aj ak al funct par_A par_B 1 2 3 4 1 gd_12 gd_17 2 3 4 5 1 gd_17 gd_17 Also here the example for Gromos forcefield but I am using OPLS force field so I assume these numbers will be different as well. How can I find the parameters for B state for OPLS force field? All of that information is in ffbonded.itp, as it is for all force fields. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Is version 5.0 generating portable binaries?
On Jan 30, 2014 11:57 PM, Raffaella D'Auria rdau...@ucla.edu wrote: Hello All, I have just performed a fresh installation of gromacs version 4.6.5 on a heterogeneous linux cluster (running centos 6.4) . After the installation I see that the binaries, for say mdrun, work on all the machines with hardware similar to the one on which they were installed (namely AMD processor such as: Quad-Core AMD Opteron Processor 2354) but produce an illegal instruction (core dumped) when run on nodes with intel processors (such as: Intel Xeon CPU E5335 @ 2.00GHz). As suggested in the documentation ( http://www.gromacs.org/Documentation/Acceleration_and_parallelization#CPU_acceleration.3a_SSE.2c_AVX.2c_etc) I have tried to compile with GMX_CPU_ACCELERATION set to none (I have also turned down the optimization levels) with always the same result (illegal instruction) across different hardware. Is this expected behavior? If so will the binaries of version 5.* have the same portability problem? In short, yes, and yes. While discussions like http://redmine.gromacs.org/issues/1165 have taken place, nobody has decided to commit time to solving this, because the only benefit comes when the target machine architecture is variable, unknown, and there is no local mechanism in place to call the correct mdrun. This painful situation is partly created by choosing to have a heterogeneous cluster... In 5.0 you will be able to compile for SSE4.1 and avoid RDTSC with the distributable build option, but this is wasting the capabilities of the AMD processors. A second GROMACS install, together with a recommended run script that chooses the mdrun binary based on the node name / whatever should be a reasonable solution. Mark One more thing the situation described above occurs with both the gnu 4.4.7 compiler and the intel 13.1.1. Any feedback would be greatly appreciated. Thanks, Raffaella. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Simulate Lennard-Jones System
Dear users, I would like to simulate a Lennard-Jones system with one or two species of atoms. But my knowledge is only about Lennard-Jones 6-12 potential and I haven't figured out how to use that potential to set up the system with GROMACS. Could anybody help me with this? Any recommended reading material is welcome. Thanks, Zhikun -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
