[gmx-users] gmx trjconv
Dear All, I have converted a xtc file into gro file and then want to analyse it with my own fortran code. The same calculation can be done with gromacs commands from xtc file. My question is will I miss some sort of data if I use gro file as there is a precision issue between xtc and gro file ? If there is data loss is it significant enough to produce erroneous result? Thanks and regards, Dhrubajyoti Maji -- 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] problem regarding gmx trjconv
On 5/2/19 6:59 AM, Saumyak Mukherjee wrote: Dear All, I have an insulin hexamer, which (because of PBC) apparently breaks into pieces after simulation. To make the molecule whole, I use the following command: gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc cluster or gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc mol -ur compact This command(s) makes each chain (out of the 6) whole, but the chains do not come together. So the hexamer as a whole still remains broken. Is there a way to solve this problem? Use -center with an index group corresponding to residues that constitute the interface of one protein. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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] multiple replica trajectory analysis
On 5/2/19 3:19 AM, vijayakumar gosu wrote: Dear Gromacs users, I have simulated a phosphorylated protein with 3 replicas (for 300ns). I concatenated the three replicas (total 900ns) for the analysis (1_2_3_trj_50ps.xtc). When I perform analysis the protein does not include the 3 phospho residues. However when I analyzed each replica independently, protein considers all the residues including phospho residues. I am confused whether I am doing anything wrong when concatenating the trajectories. I performed analysis using 1_trj.tprfile from the first replica. Please someone suggest which .tprfile has to be used for analysis from 3 replicas. I have given a command below. echo 4 4 | gmx rms -f 1_2_3_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns Select group for output Group 0 ( System) has 43190 elements Group 1 (Protein) has 2927 elements Group 2 ( Protein-H) has 2302 elements Group 3 (C-alpha) has 292 elements Group 4 ( Backbone) has 876 elements Group 5 ( MainChain) has 1169 elements Group 6 ( MainChain+Cb) has 1443 elements Group 7 (MainChain+H) has 1454 elements Group 8 ( SideChain) has 1473 elements Group 9 (SideChain-H) has 1133 elements Group10 (Prot-Masses) has 2927 elements Group11 (non-Protein) has 40263 elements Group12 ( Other) has38 elements Group13 (T1P) has26 elements Group14 (S1P) has12 elements Group15 ( NA) has16 elements Group16 ( Water) has 40209 elements Group17 (SOL) has 40209 elements Group18 ( non-Water) has 2981 elements Group19 (Ion) has16 elements Group20 (T1P) has26 elements Group21 (S1P) has12 elements Group22 ( NA) has16 elements Group23 ( Water_and_ions) has 40225 elements If i check for independent replica, using the below command echo 4 4 | gmx rms –f 1_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns Select group for output Group 0 ( System) has 43190 elements Group 1 (Protein) has 2965 elements Group 2 ( Protein-H) has 2334 elements Group 3 (C-alpha) has 295 elements Group 4 ( Backbone) has 885 elements Group 5 ( MainChain) has 1181 elements Group 6 ( MainChain+Cb) has 1458 elements Group 7 (MainChain+H) has 1469 elements Group 8 ( SideChain) has 1496 elements Group 9 (SideChain-H) has 1153 elements Group10 (Prot-Masses) has 2965 elements Group11 (non-Protein) has 40225 elements Group12 ( Other) has 40225 elements Group13 (SOL) has 40209 elements Group14 ( NA) has16 elements is it ok to make index file (protein+phosphoresidues) for analysis of the concatenated trajectory. You can do that, or add the phosphorylated residues to residuetypes.dat. The fact that it doesn't show up in one case is mysterious, but either you are working on a different computer with a properly updated residuetypes.dat (in $GMXLIB or in the working directory) or you are using a different GROMACS version that similarly does not recognize S1P and T1P as protein residues. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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 trjconv does not produce exact .gro file (slightly different box length)
On 5/2/19 5:13 AM, Faezeh Pousaneh wrote: Hi, I notice that gmx trjconv does not produce the exact .gro file (slightly different box lengths). I mean when i run following command gmx trjconv -f NPT.trr -s NPT.tpr -o f.gro -pbc mol -b 2000 I get slightly different box length than when I run gmx energy ... and select box-X,Y,Z. Anyone knows why? .trr and .edr store greater precision. A coordinate file format like .gro has limited precision. The same thing happens with coordinates and velocities. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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] Electric field applied to a water box
Dear all, I tried to apply a static electric field across a water box. I used anisotropic pressure coupling. Details of the pressure coupling is given below. pcoupl = Parrinello-Rahman pcoupltype = anisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1.0 1.0 1.0 0 0 0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; electric-field-y = 0.1 0 0 0 I see that water box size reduced in the direction of application of electric field (Y) and increased in X and Z direction. Original Size = (4 x 4 x 4) nm Final Size = (4.3 x 2.8 x 4.9) nm I would like to know if I made an error in providing the mdp options and also the origin of the compression of water box in Y direction. Thanks a lot for your help!. Nidhin Thomas University of Houston -- 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] problem regarding gmx trjconv
Dear All, I have an insulin hexamer, which (because of PBC) apparently breaks into pieces after simulation. To make the molecule whole, I use the following command: gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc cluster or gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc mol -ur compact This command(s) makes each chain (out of the 6) whole, but the chains do not come together. So the hexamer as a whole still remains broken. Is there a way to solve this problem? Thanks and Regards, Saumyak -- === *Saumyak Mukherjee* Senior Research Fellow Solid State and Structural Chemistry Unit Indian Institute of Science Bengaluru - 560012 === -- 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] Membrane-protein Simulation
Yes it is normal to correct .xtc file through -pbc flag On Thu, May 2, 2019, 12:57 PM Sankaran SV . <119013...@sastra.ac.in> wrote: > Dear all, > > We are investigating the hydration dynamics of membrane proteins (AQP > embedded in DPPC membrane). The topology and the mdp files for simulations > was obtained from the MemprotMD database (mdp file: > http://memprotmd.bioch.ox.ac.uk/). We modified the temperature of > simulation to 310 K since we are interested in the hydration dynamics at > body temperature. After 100 ns simulations, we observe that the protein has > drifted from the center of the bilayer to the periphery. There was no > changes in the lipid layers. The apparent movement of the protein vanished > after pbc correction was performed with centering the protein. Could you > please advise if it is common to observe proteins drifting during the > simulation and if it is fine to correct it with pbc correction? > > Thanks. > -- > 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] multiple replica trajectory analysis
When you are trying to join two .xtc files phosphorylated residues will be broken. They remain intact when you generate the pdb files or any other analysis.xvg from one and single .xtc file that you have suggested before running md simulation On Thu, May 2, 2019, 12:19 PM vijayakumar gosu wrote: > Dear Gromacs users, > > > > I have simulated a phosphorylated protein with 3 replicas (for 300ns). I > concatenated the three replicas (total 900ns) for the analysis > (1_2_3_trj_50ps.xtc). When I perform analysis the protein does not include > the 3 phospho residues. However when I analyzed each replica independently, > protein considers all the residues including phospho residues. I am > confused whether I am doing anything wrong when concatenating the > trajectories. I performed analysis using 1_trj.tprfile from the first > replica. Please someone suggest which .tprfile has to be used for analysis > from 3 replicas. I have given a command below. > > > echo 4 4 | gmx rms -f 1_2_3_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns > > Select group for output > > Group 0 ( System) has 43190 elements > > Group 1 (Protein) has 2927 elements > > Group 2 ( Protein-H) has 2302 elements > > Group 3 (C-alpha) has 292 elements > > Group 4 ( Backbone) has 876 elements > > Group 5 ( MainChain) has 1169 elements > > Group 6 ( MainChain+Cb) has 1443 elements > > Group 7 (MainChain+H) has 1454 elements > > Group 8 ( SideChain) has 1473 elements > > Group 9 (SideChain-H) has 1133 elements > > Group10 (Prot-Masses) has 2927 elements > > Group11 (non-Protein) has 40263 elements > > Group12 ( Other) has38 elements > > Group13 (T1P) has26 elements > > Group14 (S1P) has12 elements > > Group15 ( NA) has16 elements > > Group16 ( Water) has 40209 elements > > Group17 (SOL) has 40209 elements > > Group18 ( non-Water) has 2981 elements > > Group19 (Ion) has16 elements > > Group20 (T1P) has26 elements > > Group21 (S1P) has12 elements > > Group22 ( NA) has16 elements > > Group23 ( Water_and_ions) has 40225 elements > > > If i check for independent replica, using the below command > > echo 4 4 | gmx rms –f 1_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns > > Select group for output > > Group 0 ( System) has 43190 elements > > Group 1 (Protein) has 2965 elements > > Group 2 ( Protein-H) has 2334 elements > > Group 3 (C-alpha) has 295 elements > > Group 4 ( Backbone) has 885 elements > > Group 5 ( MainChain) has 1181 elements > > Group 6 ( MainChain+Cb) has 1458 elements > > Group 7 (MainChain+H) has 1469 elements > > Group 8 ( SideChain) has 1496 elements > > Group 9 (SideChain-H) has 1153 elements > > Group10 (Prot-Masses) has 2965 elements > > Group11 (non-Protein) has 40225 elements > > Group12 ( Other) has 40225 elements > > Group13 (SOL) has 40209 elements > > Group14 ( NA) has16 elements > > is it ok to make index file (protein+phosphoresidues) for analysis of the > concatenated trajectory. > > Please advise me > > Thanks a lot > Gosu > -- > 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] gmx trjconv does not produce exact .gro file (slightly different box length)
Hi, I notice that gmx trjconv does not produce the exact .gro file (slightly different box lengths). I mean when i run following command gmx trjconv -f NPT.trr -s NPT.tpr -o f.gro -pbc mol -b 2000 I get slightly different box length than when I run gmx energy ... and select box-X,Y,Z. Anyone knows why? (I should add that I have tried looking at different frames and different choices in -pbc flag, but still see the problem ) Best regards --- Faezeh Pousaneh Postdoc researcher Department of Mechanical and Industrial Engineering Room 219, Gløshaugen, Richard birkelands vei 2b NTNU, Trondheim, Norway -- 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] Membrane-protein Simulation
Dear all, We are investigating the hydration dynamics of membrane proteins (AQP embedded in DPPC membrane). The topology and the mdp files for simulations was obtained from the MemprotMD database (mdp file: http://memprotmd.bioch.ox.ac.uk/). We modified the temperature of simulation to 310 K since we are interested in the hydration dynamics at body temperature. After 100 ns simulations, we observe that the protein has drifted from the center of the bilayer to the periphery. There was no changes in the lipid layers. The apparent movement of the protein vanished after pbc correction was performed with centering the protein. Could you please advise if it is common to observe proteins drifting during the simulation and if it is fine to correct it with pbc correction? Thanks. -- 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] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)
Power9 (for HPC) is 4-way SMT, so make sure to try 1,2, and 4 threads per
core (stride 4, 2, and 1 respectively). Especially if you are offloading
all force computing to the GPU, what remains on the couch may not be able
to benefit from more than 1-2 threads per core.
--
Szilárd
On Thu, May 2, 2019, 01:19 Alex wrote:
> Well, unless something important has changed within a year, I distinctly
> remember being advised here not to offload anything to GPU for EM. Not
> that we ever needed to, to be honest...
>
> In any case, we appear to be dealing with build issues here.
>
> Alex
>
> On 5/1/2019 5:09 PM, Kevin Boyd wrote:
> > Hi,
> >
> >> Of course, i am not. This is the EM. ;)
> > I haven't looked back at the code, but IIRC EM can use GPUs for the
> > nonbondeds, just not the PME. I just double-checked on one of my systems
> > with 10 cores and a GTX 1080 Ti, offloading to the GPU more than doubled
> > the minimization speed.
> >
> > Kevin
> >
> > On Wed, May 1, 2019 at 6:33 PM Alex wrote:
> >
> >> Of course, i am not. This is the EM. ;)
> >>
> >> On Wed, May 1, 2019, 4:30 PM Kevin Boyd wrote:
> >>
> >>> Hi,
> >>>
> >>> In addition to what Mark said (and I've also found pinning to be
> critical
> >>> for performance), you're also not using the GPUs with "-pme cpu -nb
> cpu".
> >>>
> >>> Kevin
> >>>
> >>> On Wed, May 1, 2019 at 5:56 PM Alex wrote:
> >>>
> Well, my experience so far has been with the EM, because the rest of
> >> the
> script (with all the dynamic things) needed that to finish. And it
> "finished" by hitting the wall. However, your comment does touch upon
> >>> what
> to do with thread pinning and I will try to set '-pin on' throughout
> to
> >>> see
> if things make a difference for the better. I am less confident about
> setting strides because it is unclear what the job manager provides in
> terms of the available core numbers. I will play around some more and
> report here.
>
> Thanks!
>
> Alex
>
> On Wed, May 1, 2019 at 3:49 PM Mark Abraham >
> wrote:
>
> > Hi,
> >
> > As with x86, GROMACS uses SIMD intrinsics on POWER9 and is thus
> >> fairly
> > insensitive to the compiler's vectorisation abilities. GCC is the
> >> only
> > compiler we've tested, as xlc can't compile simple C++11. As
> >>> everywhere,
> > you should use the latest version of gcc, as IBM spent quite some
> >> years
> > landing improvements for POWER9.
> >
> > EM is useless as a performance indicator of a dynamical simulation,
> >>> avoid
> > that - it runs serial code much much more often.
> >
> > Your run deliberately didn't fill the available cores, so just like
> >> on
> x86,
> > mdrun will leave the thread affinity handling to the environment,
> >> which
> is
> > often a path to bad performance. So, if you plan on doing that often,
> > you'll want to check out the mdrun performance guide docs about the
> >>> mdrun
> > -pin and related options.
> >
> > Mark
> >
> >
> > On Wed., 1 May 2019, 23:21 Alex, wrote:
> >
> >> Hi all,
> >>
> >> Our institution decided to be all fancy, so now we have a bunch of
> Power9
> >> nodes, each with 80 cores + 4 Volta GPUs. Stuff is managed by
> >> slurm.
> > Today
> >> I did a simple EM ('gmx mdrun -ntomp 4 -ntmpi 4 -pme cpu -nb cpu')
> >>> and
> > the
> >> performance is abysmal, I would guess 100 times slower than on
> >>> anything
> >> I've ever seen before.
> >>
> >> Our admin person emailed me the following:
> >> "-- it would not surprise me if the GCC compilers were relatively
> >> bad
> at
> >> taking advantage of POWER9 vectorization, they're likely optimized
> >>> for
> >> x86_64 vector stuff like SSE and AVX operations. This was an issue
> >>> in
> > the
> >> build, I selected "-DGMX_SIMD=IBM_VSX" for the config, but
> >> according
> >>> to
> > my
> >> notes, that was part of an attempt to fix the "unimplemented SIMD"
> error
> >> that was dogging me at first, and/but which was eventually cleared
> >> by
> >> switching to gcc-6."
> >>
> >> Does anyone have any comments/suggestions on building and running
> >> GMX
> on
> >> Power9?
> >>
> >> Thank you,
> >>
> >> Alex
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >>
> >>
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Ckevin.boyd%40uconn.edu%7C5ae99d654910469ebe9008d6ce8502d1%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636923468018052656sdata=zejDS0OvUCl%2BSch%2BzVtxic%2B%2BDFIPEhB1DygmpmQ2dvw%3Dreserved=0
> before
> >> posting!
> >>
> >> * Can't post? Read
> >>
>
[gmx-users] multiple replica trajectory analysis
Dear Gromacs users, I have simulated a phosphorylated protein with 3 replicas (for 300ns). I concatenated the three replicas (total 900ns) for the analysis (1_2_3_trj_50ps.xtc). When I perform analysis the protein does not include the 3 phospho residues. However when I analyzed each replica independently, protein considers all the residues including phospho residues. I am confused whether I am doing anything wrong when concatenating the trajectories. I performed analysis using 1_trj.tprfile from the first replica. Please someone suggest which .tprfile has to be used for analysis from 3 replicas. I have given a command below. echo 4 4 | gmx rms -f 1_2_3_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns Select group for output Group 0 ( System) has 43190 elements Group 1 (Protein) has 2927 elements Group 2 ( Protein-H) has 2302 elements Group 3 (C-alpha) has 292 elements Group 4 ( Backbone) has 876 elements Group 5 ( MainChain) has 1169 elements Group 6 ( MainChain+Cb) has 1443 elements Group 7 (MainChain+H) has 1454 elements Group 8 ( SideChain) has 1473 elements Group 9 (SideChain-H) has 1133 elements Group10 (Prot-Masses) has 2927 elements Group11 (non-Protein) has 40263 elements Group12 ( Other) has38 elements Group13 (T1P) has26 elements Group14 (S1P) has12 elements Group15 ( NA) has16 elements Group16 ( Water) has 40209 elements Group17 (SOL) has 40209 elements Group18 ( non-Water) has 2981 elements Group19 (Ion) has16 elements Group20 (T1P) has26 elements Group21 (S1P) has12 elements Group22 ( NA) has16 elements Group23 ( Water_and_ions) has 40225 elements If i check for independent replica, using the below command echo 4 4 | gmx rms –f 1_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns Select group for output Group 0 ( System) has 43190 elements Group 1 (Protein) has 2965 elements Group 2 ( Protein-H) has 2334 elements Group 3 (C-alpha) has 295 elements Group 4 ( Backbone) has 885 elements Group 5 ( MainChain) has 1181 elements Group 6 ( MainChain+Cb) has 1458 elements Group 7 (MainChain+H) has 1469 elements Group 8 ( SideChain) has 1496 elements Group 9 (SideChain-H) has 1153 elements Group10 (Prot-Masses) has 2965 elements Group11 (non-Protein) has 40225 elements Group12 ( Other) has 40225 elements Group13 (SOL) has 40209 elements Group14 ( NA) has16 elements is it ok to make index file (protein+phosphoresidues) for analysis of the concatenated trajectory. Please advise me Thanks a lot Gosu -- 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] 2019.2 build warnings
Hi Szilárd, Thanks a bunch. I have upgraded to 2019.2 and a fairly large "production" test seems to be running without any issues. Alex On 5/1/2019 5:07 AM, Szilárd Páll wrote: Hi, You can safely ignore the errors as these are caused by properties of your hardware that the test scripts are not dealing well enough -- though admittedly, two of the three errors should be avoided along a message similar to this "Mdrun cannot use the requested (or automatic) number of OpenMP threads, retrying with 8." (which is what I get when I run the tests on a similar machine). If you need the tests to pass on the node in question, let me know, I can suggest workarounds. Cheers, -- Szilárd On Mon, Apr 29, 2019 at 6:47 PM Alex wrote: Hi Szilárd, Since I don't know which directory inside /complex corresponds to which tests (at least one of the tests that failed was #42), here's a tarball of the entire /complex directory per location you specified below: https://www.dropbox.com/s/44uluopkdan2417/regression_complex_2019.2.tar.gz?dl=0 If you can help us figure this out, it will be great! Thanks, Alex On 4/29/2019 4:25 AM, Szilárd Páll wrote: Hi, I assume you used -DREGRESSIONTEST_DOWNLOAD=ON case in which the tests are downloaded and unpacked under BUILD_TREE/tests/regressiontests-release-2019-[SUFFIX]/ In that directory you find the usual regressiontests tree, from there under complex/ you'll find the tests in question. Cheers, -- Szilárd On Fri, Apr 26, 2019 at 7:00 PM Alex wrote: Hi Szilárd, I am at a conference right now, but will do my best to upload the requested data first thing on Monday. In the meantime, could you please tell me where the stuff of interest would be located within the local gromacs build directory? I mean, I could make the entire directory a tarball, but not sure it's all that necessary. I don't remember which tests failed, unfortunately... Thank you! Alex On 4/25/2019 2:54 AM, Szilárd Páll wrote: Hi Alex, On Wed, Apr 24, 2019 at 9:59 PM Alex wrote: Hi Szilárd, We are using neither Ubuntu 18.04, nor glibc 2.27, but the problem is most certainly there. OK. Can you please post the content of the directories of tests that failed? It would be useful to know the exact software configuration (reported in the log) and the details of the errors (reported in the mdrun.out). Thanks, -- Szilárd Until the issue is solved one way or another, we will be staying with 2018.1, i guess. $ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description:Ubuntu 16.04.6 LTS Release:16.04 Codename: xenial Ubuntu GLIBC 2.23-0ubuntu11 On 4/24/2019 4:57 AM, Szilárd Páll wrote: What OS are you using? There are some known issues with the Ubuntu 18.04 + glibc 2.27 which could explain the errors. -- Szilárd -- 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. -- 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.
