[gmx-users] H-bond analysis
hi, I try to analyze H-bonds in an MD trajectory. when i look at the definition of an H-bond used by g_hbond it appears that only three atoms (acceptor, donor, hydrogen, ADH) are used in the analysis performed by this program ... however, i would assume that in fact 4 (or up to 6) atoms should be considered because the existence and the strength of an H-bond not only depend on the A-D distance and the ADH angle but also on the orientation of the lone pairs of the acceptor, and the latter are actually determined by the geometry of the atom(s), call them X, the acceptor is covalently bound to, aren't they? So, in short, my question is: is anybody aware of a tool that can analyze the H-bonds in MD trajectories considering not only A-D distance and ADH angle but also the position of X (basically the dihedral DHAX) ? thanks for any hints cheers, michael -- View this message in context: http://gromacs.5086.x6.nabble.com/H-bond-analysis-tp5015899.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] a gromacs feature to do TMD like simulation
did you look at the documentation for the pull code? generally you want to be careful interpreting such calculations ... the parameters for commonly used protein force fields were fitted to reproduce equilibrium structures ... even if they were, in principle, applicable to what's in between (transition state geometries) this would still leave the problem that in most cases the structures of such transition states are poorly defined. In particular for a transition involving an extensive rearrangement of a protein loop there is a myriad of potential pathways to go from one equilibrium state to another, and you'd have to obtain a thorough sampling of these pathways to get a meaningful answer to your question - this might turn out prohibitive in view of the required simulation times ... cheers mic -- View this message in context: http://gromacs.5086.x6.nabble.com/a-gromacs-feature-to-do-TMD-like-simulation-tp5015615p5015644.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] Can Ryckaert-Bellemans(RB) function be used to calculate improper dihedrals?
i was wondering about the same question ... from using antechamber and amb2gmx.pl output in simulations i concluded that this seems to work, in other words the R-B dihedrals are in fact used for improper dihedrals, you can check by looking at your topology files ... for improper dihedrals the central atom is usually the third (ak) of the four numbers in your topology file ... [ dihedrals ] ; aiajakal functc0c1c2 c3 3 2 1 5 3myimp-x-x-x-x the fact that this comes under the heading [ dihedrals ] is confusing but harmless in my experience .. if you use pdb2gmx you also need to make sure that in the top section of your rtp file type 3 is requested for impropers! cheers mic -- View this message in context: http://gromacs.5086.x6.nabble.com/Can-Ryckaert-Bellemans-RB-function-be-used-to-calculate-improper-dihedrals-tp5015630p5015643.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] how to create a PEO Residue database
for a template and instructions for making a polymer residue database based on opls you also might want to have a look at gmx-ffoplsp in http://brunsteiner.net/software.html this worked for gmx-4.0.7 and should still do so, only you don't need to edit the FF.dat file anymore but just insert a folder containing the required files (essentially rtp, atomtypes, ffbonded, and ffnonbonded) in the share/gromacs/top directory, the folder is called name.ff where "name" is randomly chosen identifyer for you ff ... cheers -- View this message in context: http://gromacs.5086.x6.nabble.com/how-to-create-a-PEO-Residue-database-tp4436179p5015642.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] energy groups/GPU and 4.6 vs 5.0
thanks for the reply! ... to be precise i should add that when i say analyze i actually mean rerun 4.5.6 trajectories with mdrun-5.0-breta ... cheers michael -- View this message in context: http://gromacs.5086.x6.nabble.com/energy-groups-GPU-and-4-6-vs-5-0-tp5015634p5015640.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.
[gmx-users] energy groups/GPU and 4.6 vs 5.0
two questions: 1) searching this list if found this comment: "NOTE: With GPUs, reporting energy group contributions is not supported" this was true for version 4.6.1 is it still the case for 4.6.5 and/or for 5.0-beta? 2) if i use mdrun-5.0-beta to analzye trajectories produced with 4.6.5 do i have to expect any kind of issues? thanks! michael -- View this message in context: http://gromacs.5086.x6.nabble.com/energy-groups-GPU-and-4-6-vs-5-0-tp5015634.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] compilation error with gcc in non-standard location
thanks for both replies ... -DGMX_CPU_ACCELERATION=SSE2 did the trick ... regards michael -- View this message in context: http://gromacs.5086.x6.nabble.com/compilation-error-with-gcc-in-non-standard-location-tp5015385p5015415.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.
[gmx-users] compilation error with gcc in non-standard location
Hi, trying to install gmx-4.6.5 i use cmake as in CMAKE_PREFIX_PATH=/home/micb/local cmake ../gromacs-4.6.5 -DGMX_GPU=OFF -DGMX_MPI=OFF -DCMAKE_INSTALL_PREFIX=/home/micb/local -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_CPU_ACCELERATION=SSE2 this gives me: [...] -- Performing Test GNU_SSE4_CFLAG -- Performing Test GNU_SSE4_CFLAG - Failed CMake Warning at CMakeLists.txt:708 (message): No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance -- Looking for smmintrin.h -- Looking for smmintrin.h - not found CMake Error at CMakeLists.txt:731 (message): Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support. -- Configuring incomplete, errors occurred! i get the same kind of error both with and w/o the -DCMAKE_CPU_ACCELERATION=SSE2 flag. i believve the problem might be that i try using a gcc that is not in the standard location. Because gcc-4.8 was not available on the machine in question (a rocks cluster) i installed gcc-4.8 with the prefix /home/micb/local and set the PATH so that gcc, g++, etc version 4.8 are used ... smmintrin.h is actually there but it is in: /home/micb/local/lib/gcc/x86_64-unknown-linux-gnu/4.8.2/include and even if i precede the cmake command by: CMAKE_INCLUDE_PATH=/home/micb/local/lib/gcc/x86_64-unknown-linux-gnu/4.8.2/include i get exactly the same error ... what am i missing? thanks! michael -- View this message in context: http://gromacs.5086.x6.nabble.com/compilation-error-with-gcc-in-non-standard-location-tp5015385.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] segmentation fault in vanilla TI calculation, death without further noitice
figured it out ... the new soft core thingy (48-1) does not seem to be very stable at single precision ... if i use sc-alpha = 0.5 sc-r-power = 6 instead of sc-alpha = 0.002 sc-r-power = 48 it seems to work this has in fact been observed earlier ... see the comments in the ethanol solvation free energy example at alchemistry.org mic -- View this message in context: http://gromacs.5086.x6.nabble.com/segmentation-fault-in-vanilla-TI-calculation-death-without-further-noitice-tp5015242p5015247.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.
[gmx-users] segmentation fault in vanilla TI calculation, death without further noitice
dear all, i performed a simple test for free energy calculations turning off one water molecule to determine the chemical potential of water. I start from a well equilibrated water box. At lambda=1.0 (the fully coupled state) the simulation stops and dies at the first step without any error messages or warnings. With the other lambda states (lambda<1.0) things work fine. I do get a warning from grompp: "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used" which i ignore as the state lambda=0 is NOT nearly decoupled. in the log file the energies at step 0 are printed (they look "normal") then nothing further stdout is: [...] step 0 NOTE: Turning on dynamic load balancing Segmentation fault (core dumped) below are my mdp and topology files any help is appreciated! thanks, michael mdp: integrator = md dt = 0.002 nsteps = 10 comm-grps= System ; nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy= 100 ; nstlist = 20 ns_type = grid pbc = xyz r_list = 1.2 ;cutoff-scheme= Verlet ; coulombtype = PME rcoulomb = 1.2 vdw_type = cut-off rvdw = 1.2 DispCorr = No ; tcoupl = v-rescale tc-grps = Water few tau_t= 0.2 0.2 ref_t= 298.0 298.0 ; gen-vel = yes gen-temp = 240.0 gen-seed = 45411 ; Pcoupl = berendsen Pcoupltype = isotropic tau_p= 0.4 compressibility = 1.0e-5 ref_p= 1.0 ; free-energy = yes init-lambda-state= 10 delta-lambda = 0 coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 vdw-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 calc-lambda-neighbors= 1 sc-alpha = 0.002 sc-r-power = 48 sc-coul = yes sc-power = 1 sc-sigma = 0.3 couple-moltype = few couple-lambda0 = none couple-lambda1 = vdw-q couple-intramol = no nstdhdl = 100 constraints = all-bonds constraint-algorithm = LINCS continuation = no top: #define _FF_AMBER #define _FF_AMBER03 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ; name at.num mass charge ptype sigma epsilon OW 8 16.000. A 3.15061e-01 6.36386e-01 HW 1 1.008 0. A 0.0e+00 0.0e+00 [ moleculetype ] ; molname nrexcl wat 2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW 1 SOL OW 1 -0.83416.0 2 HW 1 SOL HW1 1 0.417 1.00800 3 HW 1 SOL HW2 1 0.417 1.00800 [ settles ] ; OWfunct doh dhh 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 [ moleculetype ] ; molname nrexcl few 2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW 1 few OW 1 -0.83416.0 2 HW 1 few HW1 1 0.417 1.00800 3 HW 1 few HW2 1 0.417 1.00800 [ bonds ] ; i j funct length force_constant 1 2 1 0.09572 502416.0 1 3 1 0.09572 502416.0 2 3 1 0.15139 502416.0 ;[ constraints ] ; 1 2 1 ; 1 3 1 ; 2 3 1 [ exclusions ] 1 2 3 2 1 3 3 1 2 [ system ] ; Name w1k [ molecules ] ; Compound#mols wat 999 few 1 -- View this message in context: http://gromacs.5086.x6.nabble.com/segmentation-fault-in-vanilla-TI-calculation-death-without-further-noitice-tp5015242.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.
[gmx-users] free energy calculations
three questions regarding free energy calculations ... 1) i try running a free energy calculation and get an error msg: "The Verlet cut-off scheme does not (yet) support free-energy calculations with perturbed atoms, only perturbed interactions. This will be implemented soon. Use the group scheme for now." in my top file i simply defined typeB, chargeB, massB for a particular molecule, my mdp file is below ... what is the difference between "perturbed interactions" and "perturbed atoms"?? 2) if i turn OFF a molecule turning all atoms in this molecule into dummy types with zero charge and vdw epsilon=0 ... do i have to explicitely tell gmx about the bonded-interactions between the various dummy atoms, or is gmx smart enough to simply use the original parameters from the un-perturbed molecule? does "couple-moltype" help here ?? 3) is there anywhere such a thing as a tutorial for advanced free energy methods, in particular i'd be interested in trying expanded ensembles/hamiltonian exchange ... thanks! michael mdp file: integrator = sd dt = 0.002 nsteps = 10 comm-grps= System ; nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy= 100 ; nstlist = 20 ns_type = grid pbc = xyz cutoff-scheme= Verlet ; coulombtype = PME rcoulomb = 1.2 vdw_type = cut-off rvdw = 1.2 DispCorr = No ; tc-grps = Other wat tau_t= 0.2 0.2 ref_t= 298.0 298.0 ; gen-vel = yes gen-temp = 40.0 gen-seed = 45411 continuation = no ; Pcoupl = berendsen Pcoupltype = anisotropic tau_p= 0.4 0.4 0.4 0.0 0.0 0.0 compressibility = 1.0e-5 1.0e-5 1.0e-5 0.0 0.0 0.0 ref_p= 1.0 1.0 1.0 0.0 0.0 0.0 ; constraints = h-bonds constraint-algorithm = LINCS ; free-energy = yes init-lambda-state= 0 delta-lambda = 0 coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 vdw-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 calc-lambda-neighbors= -1 sc-alpha = 0.002 sc-r-power = 48 sc-coul = yes sc-power = 1 sc-sigma = 0.3 nstdhdl = 100 -- View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-calculations-tp5015229.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.
[gmx-users] multi threading on rocks cluster
dear all, I have a problem with multithreading on a cluster. Our (vanilla) rocks cluster has several nodes each with 8 cores. I used to be able to start a job with "mdrun_d -nt 8" (NOT mdrun_mpi) and the directive "-pe mpi_smp 8" in the qsub job file, and the calculations would automatically be distributed over the eight cores in a single node. Now judging from the speed of calculations, it seems as if only one core was used, but in the log file there is a statement: "Using 8 MPI threads" ... is there any way to make sure that all cores are used, and is there a way to check how many cores are really used by a given job? thanks! michael ps: I used a tpr file made with grompp version 4.6.5 and the mdrun on the cluster is actually 4.6.3 ... mdrun does not complain, but can this be the problem? pps: i found that when using "cutoff-scheme = Verlet" in the mdp file the jobs run faster than otherwise, but even then they are slower than expected ... ppps: i these runs i do not use PME, but cut-off for electrostatics, does this perhaps affect multi-threading? -- View this message in context: http://gromacs.5086.x6.nabble.com/multi-threading-on-rocks-cluster-tp5015146.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.
