[gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 139

SHYANTANI MAITI shyantani.maiti at gmail.com
Mon Apr 30 17:36:43 CEST 2018 

Thanks for helping out. Have tried this it works fine I hope.

On Wed, Mar 28, 2018 at 12:45 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
>         gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>         gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
>         gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>    1. Re: gmx mindist error (Jo?o Henriques)
>    2. Re: Number of Xeon cores per GTX 1080Ti (Mark Abraham)
>    3. mdrun on single node with GPU (Myunggi Yi)
>    4. RMSD values consideration (SHYANTANI MAITI)
>    5. Re: RMSD values consideration (Ahmed Mashaly)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 27 Mar 2018 23:55:54 +0200
> From: Jo?o Henriques <joao.m.a.henriques at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gmx mindist error
> Message-ID:
>         <CAHv45qM2J-DE6xi43aqfkxnm38PzabRVk2NHBVBQ
> 7oGko3yV4w at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Yes, I understand what you and Justin refer to. Until your first email I
> completely forgot to consider that certain simulations require variations
> to the normal 3D periodicity, and thus my ramble about the box vectors. It
> makes perfect sense now.
>
> Also, thank you suggesting the alternative using the PDB, really
> appreciated. It can certainly make things easier in this particular case.
>
> Best regards,
> J
>
> On Tue, Mar 27, 2018 at 9:48 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Looking at the code, if your PDB file had suitable CRYST1 fields then you
> > would not have needed a .tpr. I improved the docs a bit at
> > https://gerrit.gromacs.org/#/c/7729/
> >
> > Mark
> >
> > On Tue, Mar 27, 2018 at 8:58 PM Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > I have no idea how ACEMD works, but one can certainly imagine an MD
> > > package that hard codes the assumption of a cubic box with normal 3D
> > > periodicity. But there's nothing intrinsic to the file format that
> > implies
> > > any periodicity to a box. That's either a convention, or given by other
> > > information from the user.
> > >
> > > Mark
> > >
> > > On Tue, Mar 27, 2018, 18:26 Jo?o Henriques <
> joao.m.a.henriques at gmail.com
> > >
> > > wrote:
> > >
> > >> I see, I didn't consider that. I was strictly thinking about the
> > geometry
> > >> of the box.
> > >>
> > >> Anyway, with some tricks I managed to build a tpr and am now able to
> > >> calculate the mindist to the periodic image.
> > >>
> > >> Thanks!
> > >> J
> > >>
> > >> On 18:19, Tue, Mar 27, 2018 Mark Abraham <mark.j.abraham at gmail.com>
> > >> wrote:
> > >>
> > >> > Hi,
> > >> >
> > >> > The box sizes say nothing about whether the boundary is fully or
> > >> partially
> > >> > periodic, or screw, or not.
> > >> >
> > >> > Mark
> > >> >
> > >> > On Tue, Mar 27, 2018, 16:13 Jo?o Henriques <
> > >> joao.m.a.henriques at gmail.com>
> > >> > wrote:
> > >> >
> > >> > > Thanks Justin, I was really trying to avoid making a tpr file,
> > >> because my
> > >> > > ACEMD uses the Amber format. I sort of hoped gmx mindist could
> > figure
> > >> it
> > >> > > out from the box components present in the xtc file. In principle,
> > >> > couldn't
> > >> > > it be done by using that info alone? Just curious.
> > >> > >
> > >> > > J
> > >> > >
> > >> > > On Tue, Mar 27, 2018 at 4:04 PM, Justin Lemkul <jalemkul at vt.edu>
> > >> wrote:
> > >> > >
> > >> > > >
> > >> > > >
> > >> > > > On 3/27/18 9:59 AM, Jo?o Henriques wrote:
> > >> > > >
> > >> > > >> Dear users and developers,
> > >> > > >>
> > >> > > >> I am trying to use gmx mindist to calculate the minimum
> distance
> > >> > between
> > >> > > >> periodic images but I get the following error:
> > >> > > >>
> > >> > > >> Fatal error:
> > >> > > >> pbc = no is not supported by g_mindist
> > >> > > >>
> > >> > > >> This is the command I am running:
> > >> > > >>
> > >> > > >> gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc
> > >> > > >>
> > >> > > >> Now, I have to admit that the .xtc file I'm using is generated
> by
> > >> > ACEMD
> > >> > > >> and
> > >> > > >> not mdrun, but I used gmx dump to check it and everything looks
> > >> sane.
> > >> > > The
> > >> > > >> cuboid box sizes are clearly specified and I don't understand
> > what
> > >> the
> > >> > > >> problem is...
> > >> > > >>
> > >> > > >> box (3x3):
> > >> > > >>     box[    0]={ 8.16756e+00,  0.00000e+00,  0.00000e+00}
> > >> > > >>     box[    1]={ 0.00000e+00,  8.25175e+00,  0.00000e+00}
> > >> > > >>     box[    2]={ 0.00000e+00,  0.00000e+00,  9.73586e+00}
> > >> > > >>
> > >> > > >> Is gmx mindist reading the box vector lengths from the
> structure
> > >> file
> > >> > > >> instead?
> > >> > > >>
> > >> > > >
> > >> > > > When you don't provide a .tpr file, the program does not know
> what
> > >> type
> > >> > > of
> > >> > > > periodicity the simulation used, so it cannot do the requested
> > >> > > calculation
> > >> > > > because the shifts cannot be calculated.
> > >> > > >
> > >> > > > -Justin
> > >> > > >
> > >> > > > --
> > >> > > > ==================================================
> > >> > > >
> > >> > > > Justin A. Lemkul, Ph.D.
> > >> > > > Assistant Professor
> > >> > > > Virginia Tech Department of Biochemistry
> > >> > > >
> > >> > > > 303 Engel Hall
> > >> > > > 340 West Campus Dr.
> > >> > > > Blacksburg, VA 24061
> > >> > > >
> > >> > > > jalemkul at 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-request at 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-request at 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-request at 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-request at 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 28 Mar 2018 02:31:43 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Number of Xeon cores per GTX 1080Ti
> Message-ID:
>         <CAMNuMAQuh25YUbhN4DJykWnP3Bc7KKGbthNHMEjMZwYL8RSuuQ at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub <jhub at gwdg.de> wrote:
>
> > Dear Gromacs community, dear Mark,
> >
> > Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4
> > cores does not help when using a GTX 1080Ti and PME on the GPU.
> >
>
> ... for that particular simulation system.
>
>
> > Unfortunately, there were no data points between 4 and 8 CPU cores,
> > hence it was not clear at which #cores the performance actually levels
> > off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon
> > cores does not help, if not having UB potentials, but I don't have a
> > 1080Ti at hand to test for that.
> >
>
> Those data points may not have been run. Szilard might have the data - this
> was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared.
>
>
> > So my questions are:
> >
> > - At which number of E5-26XXv4 cores does the performance for common
> > systems level off with a 1080Ti for your test system (GLIC)?
> >
> > - Does the answer depend strongly on the mdp settings (in particular on
> > the LJ cutoff)?
> >
>
> Longer LJ cutoff (e.g. from different forcefields) will certainly require
> more non-bonded work, so then fewer CPU cores would be needed to do the
> remaining non-offloaded work. However any sweet spot for a particular .tpr
> would be highly dependent on other effects, such as the ratio of solvent
> (which typically has less LJ and simpler update) to solute, or the density
> of dihedral or U-B interactions. And doing pulling or FEP is very different
> again. The sweet spot for the next project will be elsewhere, sadly.
>
> This would help us a lot when choosing the appropriate CPU for a 1080Ti.
> >
> > Many thanks for any suggestions,
> > Jochen
> >
> > --
> > ---------------------------------------------------
> > Dr. Jochen Hub
> > Computational Molecular Biophysics Group
> > Institute for Microbiology and Genetics
> > Georg-August-University of G?ttingen
> > Justus-von-Liebig-Weg 11, 37077 G?ttingen, Germany
> > <https://maps.google.com/?q=Justus-von-Liebig-Weg+11,+
> 37077+G%C3%B6ttingen,+Germany&entry=gmail&source=g>
> > .
> > Phone: +49-551-39-14189 <+49%20551%203914189>
> > http://cmb.bio.uni-goettingen.de/
> > ---------------------------------------------------
> > --
> > 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-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 27 Mar 2018 23:26:15 -0400
> From: Myunggi Yi <myunggi at pukyong.ac.kr>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] mdrun on single node with GPU
> Message-ID:
>         <CAHXfRVMM1+TW33VzjQG5VmgndCfs7scx-aU-
> X2ZgwQKCCPuziA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear users,
>
> I am running simulation with gromacs 2018.1 version
> on a computer with quad core and 1 gpu.
>
> I used to use the following command to run simulations.
>
> gmx mdrun -deffnm md
>
>
> However, this time I've got the following message.
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2018.1
> Source file: src/gromacs/taskassignment/resourcedivision.cpp (line 224)
>
> Fatal error:
> When using GPUs, setting the number of OpenMP threads without specifying
> the
> number of ranks can lead to conflicting demands. Please specify the number
> of
> thread-MPI ranks as well (option -ntmpi).
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> Can anyone help?
>
>
> Thank you for any help in advance.
>
>
> Myunggi Yi
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 28 Mar 2018 12:12:50 +0530
> From: SHYANTANI MAITI <shyantani.maiti at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] RMSD values consideration
> Message-ID:
>         <CAL54tGQy+T4F0dfQZAJiLT6BQ1JoYRa3t-HHR1W+2txVbfX+=g at mail.gmail.
> com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all,
> After using this command for computation of rmsd of backbone of protein
> protein complex consisting of three proteins :
> /home/locuz/apps/gromacs/5.1/bin/gmx_mpi rms -f md_0_1.trr -s md_0_1.tpr
> The rmsd is drastically increasing from 1 to 6 nm and after that it again
> decreases to 1nm. can I use this result for my analysis? Is the rmsd
> correctly obtained?
> --
> Best regards,
> *Shyantani Maiti*
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 28 Mar 2018 07:05:42 +0000 (UTC)
> From: Ahmed Mashaly <mashaly_1988 at yahoo.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] RMSD values consideration
> Message-ID: <1396487201.108939.1522220742138 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Try using trjconv to remove pbc before analysis
> Regards,Ahmed
>
>   On Wed, 28 Mar, 2018 at 8:43 am, SHYANTANI MAITI<shyantani.maiti at gmail.
> com> wrote:   Dear all,
> After using this command for computation of rmsd of backbone of protein
> protein complex consisting of three proteins :
> /home/locuz/apps/gromacs/5.1/bin/gmx_mpi rms -f md_0_1.trr -s md_0_1.tpr
> The rmsd is drastically increasing from 1 to 6 nm and after that it again
> decreases to 1nm. can I use this result for my analysis? Is the rmsd
> correctly obtained?
> --
> Best regards,
> *Shyantani Maiti*
> --
> 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-request at 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-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 167, Issue 139
> *******************************************************
>



-- 
Best regards,
*Shyantani Maiti*

More information about the gromacs.org_gmx-users mailing list