[gmx-users] Timesteps don't match
Hi, when I minimize a system for 100 steps with nstxout set to 1 I expect to get a trajectory with 100 frames. However, gmxcheck reports 85 frames only and prints several weird messages that several timesteps don't match. Why is that? Tested with gromacs 4.6.5 and 5.0, serial run as well as a parallel run on 12 cores and 2 GPUs, always the same result. Cheers, Oliver -- Oliver Schillinger PhD student ICS-6 - Structural Biochemistry Building 5.8v, Room 3010 Phone: +49 2461-61-9532 Mobile: +49 172 53 27 914 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Martini force field for inhibitors
There are a few review article where the strategy and guidelines are described. You can find this material on the cgmartini.nl website. On Aug 29, 2014, at 2:03, Sridhar Kumar Kannam srisri...@gmail.com wrote: Dear Gromacs users, I have very recently started working with Gromacs and Martini force field. I am able to generate the coarse-grained model for HIV Protease (1hvr.pdb). I want to simulate the protein along with its inhibitor. Are there any guidelines for building (coarse-graining) its inhibitor ? Sorry for the naive question ... Thank you. -- Cheers !!! Sridhar Kumar Kannam :) -- 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] Timesteps don't match
On Fri, Aug 29, 2014 at 10:05 AM, Oliver Schillinger o.schillin...@fz-juelich.de wrote: Hi, when I minimize a system for 100 steps with nstxout set to 1 I expect to get a trajectory with 100 frames. nsteps is the maximum number of steps. If mdrun decides it can't make further progress, it says so in the log file. However, gmxcheck reports 85 frames only and prints several weird messages that several timesteps don't match. Why is that? Dunno, but since there's no time in a minimization, it's not important. Mark Tested with gromacs 4.6.5 and 5.0, serial run as well as a parallel run on 12 cores and 2 GPUs, always the same result. Cheers, Oliver -- Oliver Schillinger PhD student ICS-6 - Structural Biochemistry Building 5.8v, Room 3010 Phone: +49 2461-61-9532 Mobile: +49 172 53 27 914 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] GPU Acceleration in case of Implicit Solvent Simulations
On Thu, Aug 28, 2014 at 11:59 PM, Siva Dasetty sdas...@g.clemson.edu wrote: Dear all, Can we use periodic boundary conditions in case of implicit solvent simulations? Yes (but I only recommend doing so in GROMACS 4.5.x) If so, why? In general, why not? It's a boundary condition. What's special about infinite boundary conditions? Also, can implicit solvent model in gromacs in any version (till 5.0) be implemented in more than 2 processors or can it at least use GPU acceleration provided by gromacs? No - the implicit solvent code has been unmaintained in practice, starting with 4.6. Last I looked, only infinite boundary conditions and a single thread worked. You'll probably get better mileage on GPUs with AMBER, which actively targets this type of simulation. I have tried using pbc=no and group cut-off scheme in gpu based gromacs V5.0, but there is a warning which says GPU is disabled because it effectively works only with verlet cut-off scheme and verlet cut-off scheme requires pbc=xyz or xy. Correct. In 4.6 and 5.0, the required machinery for using GPUs and doing implicit solvation are almost completely mismatched. Mark Also tried implementing in gromacs version 4.5.5 using openMM after following the installation instructions in the following link, ( http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM ) and here again there is no luck as we dont have the compatible hardware. Thanks, Siva -- 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] Timesteps don't match
Ok yes, I got that. I should have made it clearer. The minimization actually run for 100 steps and did not converge. But that is a different issue. My probelm is that it run for 100 steps according to the log file, but there are only 85 frames in the trajectory file even though nstxout was set to 1. What happened to the rest? On 08/29/2014 11:10 AM, Mark Abraham wrote: On Fri, Aug 29, 2014 at 10:05 AM, Oliver Schillinger o.schillin...@fz-juelich.de wrote: Hi, when I minimize a system for 100 steps with nstxout set to 1 I expect to get a trajectory with 100 frames. nsteps is the maximum number of steps. If mdrun decides it can't make further progress, it says so in the log file. However, gmxcheck reports 85 frames only and prints several weird messages that several timesteps don't match. Why is that? Dunno, but since there's no time in a minimization, it's not important. Mark Tested with gromacs 4.6.5 and 5.0, serial run as well as a parallel run on 12 cores and 2 GPUs, always the same result. Cheers, Oliver -- Oliver Schillinger PhD student ICS-6 - Structural Biochemistry Building 5.8v, Room 3010 Phone: +49 2461-61-9532 Mobile: +49 172 53 27 914 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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. -- Oliver Schillinger PhD student ICS-6 - Structural Biochemistry Building 5.8v, Room 3010 Phone: +49 2461-61-9532 Mobile: +49 172 53 27 914 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] X-ray Diffraction (XRD)
Hi everyone. Does anyone know of any function in GROMACS or other MD program for generating X-ray diffraction patterns? / Cyrus -- 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] GPU and MPI
Dear users, I recently try to run Gromacs on two nodes, each of them has 12 cores and 2 GPUs. The nodes are connected with infiniband and scaling is pretty good when no GPU is evolved. My command is like this: mpiexec -npernode 2 -np 4 mdrun_mpi -ntomp 6 However, it looks like Gromacs only detected 2 GPUs on node 0, then skip node 1. Part of the output looks like: Using 4 MPI processes Using 6 OpenMP threads per MPI process 2 GPUs detected on host n0316.ten: #0: NVIDIA Tesla M2070, compute cap.: 2.0, ECC: yes, stat: compatible #1: NVIDIA Tesla M2070, compute cap.: 2.0, ECC: yes, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 2 PP ranks in this node: #0, #1 The performance is about only 40% of the run, where I use only 1 node (12 cores+2GPUs). Does I miss something? thanks. dawei -- 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] GPU and MPI
Hi Dawei, the mapping of GPUs to PP ranks is printed for the Master node only, but if this node reports two GPUs, then all other PP ranks will also use two GPUs (or an error is reported). The scaling will depend also on your system size, if this is too small, then you might be better off by using a single node. Carsten On 29 Aug 2014, at 16:24, Da-Wei Li lida...@gmail.com wrote: Dear users, I recently try to run Gromacs on two nodes, each of them has 12 cores and 2 GPUs. The nodes are connected with infiniband and scaling is pretty good when no GPU is evolved. My command is like this: mpiexec -npernode 2 -np 4 mdrun_mpi -ntomp 6 However, it looks like Gromacs only detected 2 GPUs on node 0, then skip node 1. Part of the output looks like: Using 4 MPI processes Using 6 OpenMP threads per MPI process 2 GPUs detected on host n0316.ten: #0: NVIDIA Tesla M2070, compute cap.: 2.0, ECC: yes, stat: compatible #1: NVIDIA Tesla M2070, compute cap.: 2.0, ECC: yes, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 2 PP ranks in this node: #0, #1 The performance is about only 40% of the run, where I use only 1 node (12 cores+2GPUs). Does I miss something? thanks. dawei -- 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] Pull_geometry=cylinder
Hello,I want to calculate PMF of DNA and lipid bilayer. DNA is 4.5 nm from the center of bilayer at t=0. I use the pull-code to bring closer DNA to the bilayer .This is my mdp.file: pull = umbrellapull_geometry = cylinderpull_dim = N N Ypull-r1 = 1.2pull-r0 = 1.7pull_start = yespull_nstxout = 500pull_nstfout = 500pull_ngroups = 1pull_group0 = POPCpull_group1 = DNApull_pbcatom1 = 178pull_vec1 = 0.0 0.0 1.0 ;(z-coordinate of DNAz-coordinate of POPC bilayer)pull_rate1 = 0.005pull-k1 = 500 I get the following Pull group natoms pbc atom distance at start reference at t=0 0 17152 9334 1 758 178 1.249 1.249 I don't understand, why this distance at start = 1.249 and reference = 1.249. But when I use pull_geometry = distance, distance at start = 4.5, it is right! I want to use geometry=cylinder,but I think it works wrong. Also pbc atom of group0 remains the same in both case. I don't understand this. Anyone can help me? Thanks! Alex -- 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] GPU and MPI
Hi Dawei, On 29 Aug 2014, at 16:52, Da-Wei Li lida...@gmail.com wrote: Dear Carsten Thanks for the clarification. Here it is my benchmark for a small protein system (18k atoms). (1) 1 node (12 cores/node, no GPU): 50 ns/day (2) 2 nodes (12 cores/node, no GPU): 80 ns/day (3) 1 node (12 cores/node, 2 K40 GPUs/node): 100 ns/day (4) 2 nodes (12 cores/node, 2 K40 GPUs/node): 40 ns/day I send out this question because the benchmark 4 above is very suspicious. Indeed, if you get 80 ns/day without GPUs, then it should not be less with GPUs. For how many time steps do you run each of the benchmarks? Do you use the -resethway command line switch to mdrun to disregard the first half of the run (where initialization and balancing is done, you don’t want to count that in a benchmark)? Carsten But I agree size of my system may play a role. best, dawei On Fri, Aug 29, 2014 at 10:36 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Dawei, the mapping of GPUs to PP ranks is printed for the Master node only, but if this node reports two GPUs, then all other PP ranks will also use two GPUs (or an error is reported). The scaling will depend also on your system size, if this is too small, then you might be better off by using a single node. Carsten On 29 Aug 2014, at 16:24, Da-Wei Li lida...@gmail.com wrote: Dear users, I recently try to run Gromacs on two nodes, each of them has 12 cores and 2 GPUs. The nodes are connected with infiniband and scaling is pretty good when no GPU is evolved. My command is like this: mpiexec -npernode 2 -np 4 mdrun_mpi -ntomp 6 However, it looks like Gromacs only detected 2 GPUs on node 0, then skip node 1. Part of the output looks like: Using 4 MPI processes Using 6 OpenMP threads per MPI process 2 GPUs detected on host n0316.ten: #0: NVIDIA Tesla M2070, compute cap.: 2.0, ECC: yes, stat: compatible #1: NVIDIA Tesla M2070, compute cap.: 2.0, ECC: yes, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 2 PP ranks in this node: #0, #1 The performance is about only 40% of the run, where I use only 1 node (12 cores+2GPUs). Does I miss something? thanks. dawei -- 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. -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Gromacs 4.6.7 released
Hi GROMACS users, GROMACS 4.6.7 is officially released. It contains a few bug fixes, particularly with regard to correctness of hybrid MPI/OpenMP PME simulations at moderate-to-high parallelism. We encourage all users to upgrade their installations from earlier 4.6.x releases, particularly from 4.6.6 wherein some of the problems now fixed were introduced. All the applicable content updated in 4.6.7 will also be found in the 5.0.1 release, out shortly. This is (again) the last planned release for the 4.6 series. Our resources only permit us to support one stable branch, which is now that of 5.0. We might revise that and make a new 4.6.8 release if new evidence of serious problems is found. You can find the code, manual, release notes, installation instructions and test suite at the links below. Note that the tests and manual have not changed since 4.6.5. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.7.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.7 http://www.gromacs.org/Documentation/Installation_Instructions_4.6 http://gerrit.gromacs.org/download/regressiontests-4.6.7.tar.gz Happy simulating! Mark Abraham GROMACS development manager -- 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] PMF curve in umbrella sampling
Dear Users, I am doing an umbrella sampling for a protein-ligand complex, wherein I first did an SMD run for 500 ps and generated 500 configurations, the COM distances for these configurations start at 1.25nm for conf0 and so on till 6.4nm for conf500. Hence I used a 0.05nm spacing to select configurations for the umbrella sampling windows. I have currently completed running 2 windows, each window was subjected to a 5ns mdrun. This is my mdp file parameters title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250 ; 5 ns nstcomm = 10 ; Output parameters nstxout = 5 ; every 100 ps nstvout = 5 nstfout = 5000 nstxtcout = 5000 ; every 10 ps nstenergy = 5000 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance pull_dim= Y N N pull_start = yes pull_ngroups= 1 pull_group0 = Chain_A pull_group1 = NL pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 500 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps When I use g_wham to plot the histogram and PMF curve for these 2 windows, my plots don't seem to follow the general trend as given in tutorials..(figure links below). Is this discrepancy because I have used only files from 2 windows to plot these? Or are these due to some other errors in the protocol? http://i46.photobucket.com/albums/f121/fullmeasure29/histo_2win_zpsff19fe60.png http://i46.photobucket.com/albums/f121/fullmeasure29/pmf_2win_zps04adb8f7.png -- 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] PMF curve in umbrella sampling
On 8/29/14, 2:08 PM, Mana Ib wrote: Dear Users, I am doing an umbrella sampling for a protein-ligand complex, wherein I first did an SMD run for 500 ps and generated 500 configurations, the COM distances for these configurations start at 1.25nm for conf0 and so on till 6.4nm for conf500. Hence I used a 0.05nm spacing to select configurations for the umbrella sampling windows. I have currently completed running 2 windows, each window was subjected to a 5ns mdrun. This is my mdp file parameters title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250 ; 5 ns nstcomm = 10 ; Output parameters nstxout = 5 ; every 100 ps nstvout = 5 nstfout = 5000 nstxtcout = 5000 ; every 10 ps nstenergy = 5000 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance pull_dim= Y N N pull_start = yes pull_ngroups= 1 pull_group0 = Chain_A pull_group1 = NL pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 500 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps When I use g_wham to plot the histogram and PMF curve for these 2 windows, my plots don't seem to follow the general trend as given in tutorials..(figure links below). Is this discrepancy because I have used only files from 2 windows to plot these? Or are these due to some other errors in the protocol? http://i46.photobucket.com/albums/f121/fullmeasure29/histo_2win_zpsff19fe60.png http://i46.photobucket.com/albums/f121/fullmeasure29/pmf_2win_zps04adb8f7.png The two windows yield effectively overlapping distributions and a meaningless PMF. Space the windows further (0.05 nm is very tight) and run more windows for a real PMF as a function of a meaningful reaction coordinate. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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] g_select syntax
Hi, On Fri, Aug 29, 2014 at 4:19 AM, Bin Liu fdusuperstr...@gmail.com wrote: I am recently puzzled by the syntax and behaviour of g_select. I want to obtain the residue index list of LIPID whose center of mass is within 1.0 nm of the surface of protein. In my case, each LIPID molecule consists of only one residue. I wrote the selection.dat as follows, and set -selrpos to atom and -seltype to res_com. Here I think Protein is the reference group, so -selrpos should be atom because I care about the distance to its surface. LIPID is the analysis group and I care about their individual center of mass. So -seltype should be res_com. selection.dat: resname LIPID and within 1.0 of group Protein; g_select -sf selection.dat -f traj.trr -s traj.tpr -n system.ndx -oi index.dat -seltype res_com -selrpos atom Yes, this should give you what you expect. It selects all LIPID atoms that are within 1.0 nm from the protein, and then groups them by residue for the -oi output. However I tried another selection. This time instead of retrieving the residue index, I tried to retrieve the index of a key atom of the LIPID molecule. selection.dat: rdist = res_com within 1.0 of group Protein; group_C15 = (resname LIPID) and (rdist) and (name C15); group_C15; g_select -sf selection.dat -f traj.trr -s traj.tpr -n system.ndx -oi index.dat -seltype atom -selrpos atom res_com within has a different meaning from using -seltype res_com: your second selection selects all C15 atoms that are in LIPID residues, and where the center-of-mass of the whole residue is within 1 nm from the protein (the last part is the res_com within expression). -seltype res_com in the first example is equivalent to writing this, where the res_com is in a very different location: res_com of (resname LIPID and within 1.0 of group Protein) Hopefully this helps understanding where the difference between the selections comes from. I thought these two selections should give the same number of indices per frame, as the second selection merely retrieve the atom indices of the corresponding key atoms in the LIPID molecules selected by the first selection. However the first selection gives significantly more indices than the second selection does. I guess my understanding of g_select syntax might be flawed. Please point out my misunderstanding. Thank you very much. If you want to select the key atoms that match those from your first selection, you need to write something more complex: name C15 and same residue as (resname LIPID and within 1.0 of group Protein) The last selection should be self-explanatory. Hope this helps, Teemu -- 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.
