On 7/26/16 1:16 PM, Alexander Alexander wrote:
On Tue, Jul 26, 2016 at 6:07 PM, Justin Lemkul <jalem...@vt.edu> wrote:On 7/26/16 11:27 AM, Alexander Alexander wrote:Thanks. Yes indeed it is a free energy calculation in which no problem showed up in the first 6 windows where the harmonic restrains were applying on my amino acid but the DD problem came up immediately in the first windows of the removing charge. Below please find the mdp file. And If I use -ntmpi = 1 then it takes ages to finish. Although my gromcas need to be compiled again with thread-MPI .I suspect you have inconsistent usage of couple-intramol. Your long-distance LJC pairs should be a result of "couple-intramol = no" in which you get explicit intramolecular exclusions and pair interactions that occur at longer distance than normal 1-4 interactions. If you ran other systems without getting any problem, you probably had "couple-intramol = yes" in which all nonbonded interactions are treated the same way and the bonded topology is the same.Actually I always have had "couple-intramol = no" in all my other calculation(a single amino acid in water solution), and not problem has shown up. But FEP calculations of the charged amino acid where I have also an Ion for neutralization of the system and "ion+amino acid" is used as "couple-moltype", this problem emerges. And if you noticed the Ion here CL is always one of the atom involving in the problem. I hope "couple-intramol = yes"can sove the problem in charged amino acid.
Well, there are implications for the results. Consider what it says in the manual. But yes, this is your problem. You've got physically separate molecules that you call one [moleculetype] for the purpose of transformation, and you're running into a problem that isn't really physically meaningful in any way.
Another question is that if really this amount of pull restrain isnecessary to be applied on my molecules (singke amino acid) before removing the charge and vdW?You're decoupling a single amino acid? What purpose do the pull restraints even serve? CA-HA, etc. should be bonded in a single amino acid, so why are you applying a pull restraint to them? I really don't understand.I want to make sure sudden conformational changes of amino acid do not occur during the perturbation. In particular, when the charge is turned off. Applying a harmonic restraint to keep the geometry the same during FEP is a well-established procedure, e.g. Deng, Y.; Roux, B. J Chem Theory Comput 2006, 2 (5), 1255. I might reduce the number of restraints to only between 1 or 2 pairs.
Preserving the A-state in the bonded topology (and using couple-intramol = no) will prevent any weirdness from happening without needing any of these restraints. As in my previous message, restraining CA-HA with a harmonic potential makes no sense at all. Those atoms have a bond between them. The pull code is not doing anything useful.
The whole task is to calculate the binding free energy of amino acid to a metal surface, although here I am still dealing with the amino acid in only water without surface yet.
I believe I've mentioned this before, but in case it got lost along the way - using the free energy decoupling technique is a very ineffective way of calculating this binding free energy. Do a PMF. It's extremely straightforward and you don't deal with any of these algorithmic problems. It will also likely converge a lot faster than try to do complex decoupling.
-Justin
Regards, Alex-Justin Best regards,Alex define = -DFLEXIBLE integrator = steep nsteps = 500000 emtol = 250 emstep = 0.001 nstenergy = 500 nstlog = 500 nstxout-compressed = 1000 constraint-algorithm = lincs constraints = h-bonds cutoff-scheme = Verlet rlist = 1.32 coulombtype = PME rcoulomb = 1.30 vdwtype = Cut-off rvdw = 1.30 DispCorr = EnerPres free-energy = yes init-lambda-state = 6 calc-lambda-neighbors = -1 restraint-lambdas = 0.0 0.2 0.4 0.6 0.8 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 coul-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0 1.0 1.0 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.2 0.3 0.35 0.4 0.5 0.6 0.7 0.8 0.9 1.0 couple-moltype = Protein_chain_A couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no nstdhdl = 100 sc-alpha = 0.5 sc-coul = no sc-power = 1 sc-sigma = 0.3 dhdl-derivatives = yes separate-dhdl-file = yes dhdl-print-energy = total pull = yes pull-ngroups = 9 pull-ncoords = 6 pull-group1-name = CA pull-group2-name = HA pull-group3-name = N pull-group4-name = C pull-group5-name = O1 pull-group6-name = O2 pull-group7-name = CZ pull-group8-name = NH1 pull-group9-name = NH2 pull-coord1-groups = 1 2 pull-coord1-type = umbrella pull-coord1-dim = Y Y Y pull-coord1-init = 0 pull-coord1-start = yes pull-coord1-geometry = distance pull-coord1-k = 0.0 pull-coord1-kB = 1000 pull-coord2-groups = 1 3 pull-coord2-type = umbrella pull-coord2-dim = Y Y Y pull-coord2-init = 0 pull-coord2-start = yes pull-coord2-geometry = distance pull-coord2-k = 0.0 pull-coord2-kB = 1000 pull-coord3-groups = 4 5 pull-coord3-type = umbrella pull-coord3-dim = Y Y Y pull-coord3-init = 0 pull-coord3-start = yes pull-coord3-geometry = distance pull-coord3-k = 0.0 pull-coord3-kB = 1000 pull-coord4-groups = 4 6 pull-coord4-type = umbrella pull-coord4-dim = Y Y Y pull-coord4-init = 0 pull-coord4-start = yes pull-coord4-geometry = distance pull-coord4-k = 0.0 pull-coord4-kB = 1000 pull-coord5-groups = 7 8 pull-coord5-type = umbrella pull-coord5-dim = Y Y Y pull-coord5-init = 0 pull-coord5-start = yes pull-coord5-geometry = distance pull-coord5-k = 0.0 pull-coord5-kB = 1000 pull-coord6-groups = 7 9 pull-coord6-type = umbrella pull-coord6-dim = Y Y Y pull-coord6-init = 0 pull-coord6-start = yes pull-coord6-geometry = distance pull-coord6-k = 0.0 pull-coord6-kB = 1000 On Tue, Jul 26, 2016 at 2:21 PM, Justin Lemkul <jalem...@vt.edu> wrote:On 7/26/16 8:17 AM, Alexander Alexander wrote: Hi,Thanks for your response. I do not know which two atoms has bonded interaction comparable with the cell size, however, based on this line in log file "two-body bonded interactions: 3.196 nm, LJC Pairs NB, atoms 24 28", I though the 24 and 28 are the couple whom their coordination are as below: 1ARG HH22 24 0.946 1.497 4.341 2CL CL 28 1.903 0.147 0.492 Indeed their geometrical distance is too big but it is normal I think. I manually changed the coordination of CL atom to bring it closer to the other one hoping solve the problem, and test it again, but, the problem is still here. You'll need to provide a full .mdp file for anyone to be able to tellanything. It looks like you're doing a free energy calculation, based on the numbers in LJC, and depending on the settings, free energy calculations may involve very long bonded interactions that make it difficult (or even impossible) to use DD, in which case you must use mdrun -ntmpi 1 to disable DD and rely only on OpenMP. Here also says "minimum initial size of 3.516 nm", but all of my cell sizeare higher than this as well. "Cell size" refers to a DD cell, not the box vectors of your system.Note that your system is nearly the same size as your limiting interactions, which may suggest that your box is too small to avoid periodicity problems, but that's an entirely separate issue. -Justin ?Thanks, Regards, Alex On Tue, Jul 26, 2016 at 12:12 PM, Mark Abraham < mark.j.abra...@gmail.com> wrote: Hi,So you know your cell dimensions, and mdrun is reporting that it can't decompose because you have a bonded interaction that is almost the length of the one of the cell dimensions. How big should that interaction distance be, and what might you do about it? Probably mdrun should be smarter about pbc and use better periodic image handling during DD setup, but you can fix that yourself before you call grompp. Mark On Tue, Jul 26, 2016 at 11:46 AM Alexander Alexander < alexanderwie...@gmail.com> wrote: Dear gromacs user,Now is more than one week that I am engaging with the fatal error due to domain decomposition, and I have not been succeeded yet, and it is more painful when I have to test different number of cpu's to see which one works in a cluster with a long queuing time, means being two or three daysin the queue just to see again the fatal error in two minutes.These are the dimensions of the cell " 3.53633, 4.17674, 4.99285", and below is the log file of my test submitted on 2 nodes with total 128 cores, I even reduced to 32 CPU's and even changed from "gmx_mpi mdrun" to"gmx mdrun", but the problem is still surviving.Please do not refer me to this link (http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm )as I know what is the problem but I can not solve it: Thanks, Regards, Alex Log file opened on Fri Jul 22 00:55:56 2016 Host: node074 pid: 12281 rank ID: 0 number of ranks: 64 GROMACS: gmx mdrun, VERSION 5.1.2 Executable: /home/fb_chem/chemsoft/lx24-amd64/gromacs-5.1.2-mpi/bin/gmx_mpi Data prefix: /home/fb_chem/chemsoft/lx24-amd64/gromacs-5.1.2-mpi Command line: gmx_mpi mdrun -ntomp 1 -deffnm min1.6 -s min1.6 GROMACS version: VERSION 5.1.2 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: disabled OpenCL support: disabled invsqrt routine: gmx_software_invsqrt(x) SIMD instructions: AVX_128_FMA FFT library: fftw-3.2.1 RDTSCP usage: enabled C++11 compilation: disabled TNG support: enabled Tracing support: disabled Built on: Thu Jun 23 14:17:43 CEST 2016 Built by: reuter@marc2-h2 [CMAKE] Build OS/arch: Linux 2.6.32-642.el6.x86_64 x86_64 Build CPU vendor: AuthenticAMD Build CPU brand: AMD Opteron(TM) Processor 6276 Build CPU family: 21 Model: 1 Stepping: 2 Build CPU features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop C compiler: /usr/lib64/ccache/cc GNU 4.4.7 C compiler flags: -mavx -mfma4 -mxop -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG -funroll-all-loops -Wno-array-bounds C++ compiler: /usr/lib64/ccache/c++ GNU 4.4.7 C++ compiler flags: -mavx -mfma4 -mxop -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function-O3 -DNDEBUG -funroll-all-loops -Wno-array-boundsBoost version: 1.55.0 (internal) Running on 2 nodes with total 128 cores, 128 logical cores Cores per node: 64 Logical cores per node: 64 Hardware detected on host node074 (the node of MPI rank 0): CPU info: Vendor: AuthenticAMD Brand: AMD Opteron(TM) Processor 6276 Family: 21 model: 1 stepping: 2 CPU features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop SIMD instructions most likely to fit this hardware: AVX_128_FMA SIMD instructions selected at GROMACS compile time: AVX_128_FMA Initializing Domain Decomposition on 64 ranks Dynamic load balancing: off Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 3.196 nm, LJC Pairs NB, atoms 24 28 multi-body bonded interactions: 0.397 nm, Ryckaert-Bell., atoms 5 13 Minimum cell size due to bonded interactions: 3.516 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nmEstimated maximum distance required for P-LINCS: 0.218 nmGuess for relative PME load: 0.19 Will use 48 particle-particle and 16 PME only ranks This is a guess, check the performance at the end of the log file Using 16 separate PME ranks, as guessed by mdrun Optimizing the DD grid for 48 cells with a minimum initial size of 3.516 nmThe maximum allowed number of cells is: X 1 Y 1 Z 1------------------------------------------------------- Program gmx mdrun, VERSION 5.1.2 Source code file: /home/alex/gromacs-5.1.2/src/gromacs/domdec/domdec.cpp, line: 6987 Fatal error: There is no domain decomposition for 48 ranks that is compatible with the given box and a minimum cell size of 3.51565 nm Change the number of ranks or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors------------------------------------------------------- -- 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. --================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
